SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Database of tumor-normal reads desmo Bioinformatics 2 03-27-2014 11:21 AM
min-coverage-normal & min-coverage-tumor in VarScan somatic Jane M Bioinformatics 2 11-20-2012 09:46 AM
what is normal.bam and how to get the file normal.bam shixinyi Bioinformatics 1 09-04-2012 05:05 AM
UnifiedGenotyper between tumor and normal kasthuri Bioinformatics 3 07-21-2012 09:47 AM
What normal biologists are up to Joann Literature Watch 0 02-16-2010 11:33 AM

Reply
 
Thread Tools
Old 04-17-2013, 10:40 AM   #1
ckr123
Junior Member
 
Location: houston

Join Date: Apr 2013
Posts: 1
Default VarScan not resetting normal

Hi, I am a newbie trying to identify somatic mutations with VarScan. I tried sending the input separately or together and encountered errors for both.

#separate pileup
samtools mpileup -uf RCRS.fa normal.sorted.bam > normal.mpileup
samtools mpileup -uf RCRS.fa tumor.sorted.bam > tumor.mpileup
java -Xmx4g -jar /bin/VarScan.v2.3.5.jar somatic normal.mpileup tumor.mpileup --output-snp sample1.snp --output-indel sample1.indel

Returned messages:
Min coverage: 8x for Normal, 6x for Tumor
Min reads2: 2
Min strands2: 1
Min var freq: 0.2
Min freq for hom: 0.75
Normal purity: 1.0
Tumor purity: 1.0
Min avg qual: 15
P-value thresh: 0.99
Somatic p-value: 0.05
Not resetting normal file because <
Exception in thread "main" java.lang.NumberFormatException: For input string: "iTG,XDP=500;I16=121,361,0,1,12370,335428,17,289,18616,900090,56,3136,8657,185009,25,625;VDB=0.0152PL�����"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:470)
at java.lang.Integer.parseInt(Integer.java:514)
at net.sf.varscan.Somatic.<init>(Somatic.java:1015)
at net.sf.varscan.VarScan.somatic(VarScan.java:282)
at net.sf.varscan.VarScan.main(VarScan.java:188)

#combined pileup
samtools mpileup -uf RCRS.fa normal.sorted.bam tumor.sorted.bam >
mpileup
java -Xmx4g -jar /bin/VarScan.v2.3.5.jar somatic mpileup --mpileup 1 --output-snp sample1.snp --output-indel sample1.indel

Message returned:
Min coverage: 8x for Normal, 6x for Tumor
Min reads2: 2
Min strands2: 1
Min var freq: 0.2
Min freq for hom: 0.75
Normal purity: 1.0
Tumor purity: 1.0
Min avg qual: 15
P-value thresh: 0.99
Somatic p-value: 0.05
Reading input from sample1.mpileup
Reading mpileup input...
Error: Invalid format or not enough samples in mpileup: �BC[=��BCFMTNOSM%##samtoolsVersion=0.1.18 (r982:295)

In both cases, I received indel and snp files, but they only have column names. I am really confused.

Thanks,
ckr123 is offline   Reply With Quote
Old 09-03-2013, 08:25 AM   #2
dkoboldt
Member
 
Location: St. Louis

Join Date: Mar 2009
Posts: 62
Default

This issue is caused by the -u parameter given to SAMtools. Remove -u and it should work fine.
dkoboldt is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:25 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO