Question: Understanding SomaticSniper output
gravatar for ttom
4.0 years ago by
ttom210 wrote:


I am trying to understand the output VCF from SomaticSniper

According to the header information from the VCF, if the sample field 'SS' shpws the variant status relative to non-adjacent Normal. 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown"

Ran SomaticSniper with the following options on exome data

somatic-sniper/build/bin/bam-somaticsniper -f Human_Decoy_REF/hs37d5.fa CGR1234tumor.bam CGR1234normal.bam SomaticSniper_CGR1234.out -F vcf

Question 1 - which are the somatic variants ?

There are 79,000 variants in the output VCF. Out of which ~50,000 of them have 'SS' as 2 in the tumor column. Are these all somatic variants ? Is it possible to have these many somatic variants in a tumor ? Or am I doing something wrong here ?

Question 2 - a very basic question. what are variants with Loss of Heterozygosity ?

I understand that a normal sample has HET genotype (0/1) and tumor sample has HOM_ALT genotype (1/1) that would be a LoF. But when a normal sample has '0/1' and tumor sample has '0/0', would that be a LoF as well ?

Would appreciate help,


somaticsniper • 1.6k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by ttom210

Ran SomaticSniper with recommended settings

 bam-somaticsniper -Q 40 -G -L -f reference.fa tumor.bam normal.bam output.txt

Now the total variants reduced to 6238 and 5824 of them have 'SS' as 2 in the tumor column

ADD REPLYlink written 4.0 years ago by ttom210
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1281 users visited in the last hour