Run Varscan all all samples we have

In [1]:
import os
import subprocess
import pandas as pd
from pandas import DataFrame as df
import time

path and tools

In [2]:
#gallus reference
galref="/home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa"

Define tumor-normal pairs

  • here because jupyter text editor is strange, e.g.: cannot write tabs...
In [3]:
sample_list=[        
    'Sample1','Sample4',
    'Sample4','Sample1',
    'Sample2','Sample5',
    'Sample5','Sample2',
    'Sample3','Sample6',
    'Sample6','Sample3',

    'DS1','DS2',
    'DS2','DS1',
    'DS3','DS1',
    'DS4','DS1',
    'DS5','DS1',
    'DS6','DS1',
    'DS7','DS1',
    'DS9','DS1',
    'DS10','DS1',
    'DS11','DS1',

    'DS14','DS15',
    'DS15','DS14',
    'DS16','DS14',
    'DS18','DS14',

    'DS26','DS27',
    'DS27','DS26',

    'DS33','DS34',
    'DS34','DS33',
    'DS35','DS33',
    'DS36','DS33',
    'DS37','DS33',

    #here is DS50 the best germline??
    'DS41','DS50',
    'DS42','DS50',
    'DS43','DS50',
    'DS44','DS50',
    'DS45','DS50',
    'DS46','DS50',
    'DS47','DS50',
    'DS48','DS50',
    'DS49','DS50',
    'DS50','DS41',

    'DS51','DS52',
    'DS52','DS51',
    'DS53','DS51',
    'DS54','DS51',
    'DS55','DS51',
    'DS56','DS51',
    'DS57','DS51',
    
    'DS58','DS59',
    'DS59','DS58',
    'DS60','DS58',
    'DS61','DS58',
    
    'DS62','DS33', #!!
    
    'DS63','DS64',
    'DS64','DS63',
    'DS65','DS63',
    
    'DS66','DS67',
    'DS67','DS66',
    'DS68','DS66',
    
    'DS69','DS70',
    'DS70','DS69',
    
    'DS71','DS72',
    'DS72','DS71'] #dont know about the newer ones

pairs=dict()
for i in xrange(len(sample_list)/2):
    pairs[sample_list[2*i]]=sample_list[2*i+1]

Run Varscan with on the fly generated pileups to save space

Build command, write it to script and then execute it

  • With less than 7GB Java virtual machine dies at startup:
    • Error occurred during initialization of VM Could not reserve enough space for object heap Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.
In [4]:
def run_varscan(tumsample,normsample):
    #input files
    norm_bam='/nagyvinyok/adat83/sotejedlik/dt40/rmdup/'+normsample+'_RMdup_picard_realign.bam'
    norm_fname=norm_bam.split('/')[-1].split('.')[0].split('_')[0]
    tum_bam='/nagyvinyok/adat83/sotejedlik/dt40/rmdup/'+tumsample+'_RMdup_picard_realign.bam'
    tum_fname=tum_bam.split('/')[-1].split('.')[0].split('_')[0]

    #pileup flags
    pup_flags=' -Q 30 -B '

    #create pileup command
    #cmd_norm='<(samtools mpileup '+ pup_flags+ ' -f ' + galref + ' -r 1:40,000,000-40,001,000 ' + norm_bam +' ) '
    #cmd_tum=' <(samtools mpileup '+ pup_flags+ ' -f ' + galref + ' -r 1:40,000,000-40,001,000 ' + tum_bam +' ) '
    cmd_norm='<(samtools mpileup '+ pup_flags+ ' -f ' + galref + ' ' + norm_bam +' ) '
    cmd_tum=' <(samtools mpileup '+ pup_flags+ ' -f ' + galref + ' ' + tum_bam +' ) '

    #varscan params
    mincov=' 5 '
    pval=' 0.9 '
    #output file
    outputdir='/nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/'
    output=outputdir+tum_fname+'_'+norm_fname+'.vsc'

    #varscan command
    cmd='time java -jar VarScan.v2.3.7.jar somatic '+ cmd_norm +' ' + cmd_tum + ' ' + output
    cmd+=' --min-coverage '+mincov+' --somatic-p-value '+ pval
    print cmd,'\n'


    #write scriptfile
    f=open(tum_fname+'_'+norm_fname+'.sh','w')
    f.write('#!/bin/bash\n')
    f.write(cmd+'\n')
    f.close()

    try:
        print subprocess.check_output(['sbatch','-C','jimgray88','--mem','7000',tum_fname+'_'+norm_fname+'.sh'],stderr=subprocess.STDOUT)
    except subprocess.CalledProcessError, e:
        print e.output
In [6]:
for tum,norm in pairs.iteritems():
    run_varscan(tum,norm)
    time.sleep(1)

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS50_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS49_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS49_DS50.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1362

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS50_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS48_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS48_DS50.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1363

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS50_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS47_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS47_DS50.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1364

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS50_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS46_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS46_DS50.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1365

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS50_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS45_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS45_DS50.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1366

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS50_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS44_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS44_DS50.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1367

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS50_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS43_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS43_DS50.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1368

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS50_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS42_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS42_DS50.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1369

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS50_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS41_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS41_DS50.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1370

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS33_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS36_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS36_DS33.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1371

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS1_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS9_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS9_DS1.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1372

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS1_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS6_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS6_DS1.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1373

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS1_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS7_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS7_DS1.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1374

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS1_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS4_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS4_DS1.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1375

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS1_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS5_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS5_DS1.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1376

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS1_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS2_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS2_DS1.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1377

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS1_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS3_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS3_DS1.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1378

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS2_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS1_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS1_DS2.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1379

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS1_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS10_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS10_DS1.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1380

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS1_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS11_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS11_DS1.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1381

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS15_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS14_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS14_DS15.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1382

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS14_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS15_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS15_DS14.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1383

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS14_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS16_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS16_DS14.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1384

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS14_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS18_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS18_DS14.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1385

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS33_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS37_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS37_DS33.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1386

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS33_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS34_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS34_DS33.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1387

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS33_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS35_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS35_DS33.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1388

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS34_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS33_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS33_DS34.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1389

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS71_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS72_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS72_DS71.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1390

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS72_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS71_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS71_DS72.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1391

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS59_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS58_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS58_DS59.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1392

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS58_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS59_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS59_DS58.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1393

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS51_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS54_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS54_DS51.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1394

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS51_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS55_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS55_DS51.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1395

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS51_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS56_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS56_DS51.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1396

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS51_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS57_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS57_DS51.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1397

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS41_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS50_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS50_DS41.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1398

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS52_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS51_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS51_DS52.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1399

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS51_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS52_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS52_DS51.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1400

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS51_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS53_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS53_DS51.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1401

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample2_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample5_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/Sample5_Sample2.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1402

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample1_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample4_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/Sample4_Sample1.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1403

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample3_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample6_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/Sample6_Sample3.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1404

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample4_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample1_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/Sample1_Sample4.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1405

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample6_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample3_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/Sample3_Sample6.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1406

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample5_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/Sample2_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/Sample2_Sample5.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1407

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS63_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS65_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS65_DS63.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1408

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS63_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS64_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS64_DS63.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1409

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS66_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS67_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS67_DS66.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1410

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS67_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS66_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS66_DS67.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1411

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS58_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS61_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS61_DS58.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1412

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS58_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS60_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS60_DS58.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1413

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS64_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS63_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS63_DS64.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1414

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS33_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS62_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS62_DS33.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1415

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS69_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS70_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS70_DS69.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1416

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS70_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS69_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS69_DS70.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1417

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS66_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS68_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS68_DS66.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1418

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS26_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS27_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS27_DS26.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1419

time java -jar VarScan.v2.3.7.jar somatic <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS27_RMdup_picard_realign.bam )   <(samtools mpileup  -Q 30 -B  -f /home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa /nagyvinyok/adat83/sotejedlik/dt40/rmdup/DS26_RMdup_picard_realign.bam )  /nagyvinyok/adat83/sotejedlik/ribli/dt40/snp/varscan/DS26_DS27.vsc --min-coverage  5  --somatic-p-value  0.9  

Submitted batch job 1420
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