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dkoboldt / varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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typos in doc #27

Open splaisan opened 7 years ago

splaisan commented 7 years ago

Thanks Dan for the great tool,

I just noticed what I think are typos in the accompanying doc bash variables with $ in front and spaces at either sides of the '=' sign

Best Stephane

http://dkoboldt.github.io/varscan/somatic-calling.html

Do NOT use any of the variant- or consensus-calling parameters. You just want the raw pileup output. This Perl snippet shows you how to pipe input from SAMtools into VarScan:
$normal_pileup = "samtools mpileup -f $reference $normal_bam";
$tumor_pileup = "samtools mpileup -f $reference $tumor_bam";

To limit the pileup to reads with mapping quality > 0 (recommended), use this variation:
$normal_pileup = "samtools mpileup -q 1 -f $reference $normal_bam";
$tumor_pileup = "samtools mpileup -q 1 -f $reference $tumor_bam";

Next, issue a system call that pipes input from these commands into VarScan :
bash -c \"java -jar VarScan.jar somatic <\($normal_pileup\) <\($tumor_pileup\) output
DarioS commented 7 years ago

The documentation states

--variants  Report only variant (SNP/indel) positions (mpileup2cns only) [0]

but this appears in the list of parameters for mpileup2indel. This appears contradictory.