Understanding SomaticSniper output

Question

[ttom]

Hi,

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,

Thanks

[ttom]

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