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Old 08-20-2012, 06:07 AM   #1
Location: spain

Join Date: Feb 2011
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Default varscan - filter out those snps close to indels


just a quick question about the somaticFilter provided by Varscan:

--indel-file File of indels for filtering nearby SNPs

What does (exactly) it mean 'nearby'? within the same read? at 'x' bp of distance?

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Old 08-21-2012, 11:36 PM   #2
Jane M
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I don't know but I am also interested in the answer...
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Old 10-22-2012, 08:13 AM   #3
Location: St. Louis

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Hey guys, thanks for this question and I'm sorry it took me this long to find it and answer! The --indel-filter parameter lets you specify a list of indels (called by VarScan pileup2indel) that will be used for filtering false positive SNPs due to local read mis-alignments due to indels. It will remove SNP calls at or within 1 bp of an indel's position (as reported in mpileup).

I'll see about making this distance a user-defined parameter in the next release.

For future help, please try to post in the VarScan Help forum:
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Old 10-28-2012, 09:43 AM   #4
Jane M
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Ok, so 'nearby' means 1bp, thank you.
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Old 11-19-2014, 01:41 AM   #5
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Default Filtering varscan variants

I would like to ask removing the snps closer to indels at 1bp thus removes a lot of snps for me. But it is not a test for false positive right? I believe if am using the local realignment around indel step with with GATK so the mis matches due to indel should not be a reason to work if you used GATK processed bam files for varscan and other standard variant calling tools. I am having typical normal/tumor sequenced at 70X for which I am calling variants with the varscan and if I do the somaticfilter with the sample.snp and sample.indel I lose a lot of SNPs. I get around 200 variants for my sample which I was thinking to be good numbers but then on annotating I miss out most on the exons. Also when I compare this results with mutect I do not get most of the mutations I receive with Mutect. So I ran again the VarScan with below command

samtools mpileup -f /scratch/GT/vdas/test_exome/exome/hg19.fa -q 1 -B /scratch/GT/vdas/pietro/exome_seq/results/N_S8980/N_S8980.realigned.recal.bam /scratch/GT/vdas/pietro/exome_seq/results/T_S7998/T_S7998.realigned.recal.bam | java -Xmx14G -jar /scratch/GT/softwares/VarScan.v2.3.6.jar somatic - /scratch/GT/vdas/pietro/exome_seq/results/varscan_out_17112014/S_313_T_soma_vcf.output --output-vcf 1 --mpileup 1 --min-var-freq 0.05 --min-coverage-normal 10 --min-coverage-tumor 8 --p-value 0.05
Now am getting the sample.snps.vcf with over 11k variants. I am thinking of not using somaticfilter, rather use process somatic to have the high confidence snps and then use script to extract most confident ones. How does this sound?
vd4mindia is offline   Reply With Quote

filtering, indels, snp, varscan

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