Question: varscan2 somatic sip
0
gravatar for fabbri.marco
8 days ago by
fabbri.marco0 wrote:

I have used varscan2 and the results below are not clear to me.I compared a tumour to a normal and I am interested in somatic mutation. The following snp is predicted as germline and I expected as somatic but it is not clear to me the reason, Any suggestions? Thanks Marco

##fileformat=VCFv4.1
##source=VarScan2##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: r
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NORMAL  TUMOR
chr12   49420661    .   G   A   .   PASS    DP=3204;SS=1;SSC=255;GPV=1E0;SPV=1.5981E-225    GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:1843:1835:2:0.11%:1595,240,2,0    0/1:.:1361:828:532:39.12%:740,88,475,57
snp varscan2 somatic • 91 views
ADD COMMENTlink modified 8 days ago • written 8 days ago by fabbri.marco0

I think that I will change my setting, since this is in my opinion is a somatic mutation, there only 2 reads in the normal sample (lymphoma). I check how to set varscan option in a way that this should be predicted as somatic. What do you think? Marco

ADD REPLYlink written 8 days ago by fabbri.marco0

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

ADD REPLYlink written 8 days ago by WouterDeCoster26k
0
gravatar for WouterDeCoster
8 days ago by
Belgium
WouterDeCoster26k wrote:

The SNP is found in both your tumor and your normal sample (both have a 0/1 genotype). Therefore it's not somatic but germline.

ADD COMMENTlink written 8 days ago by WouterDeCoster26k
1

The allel frequency in the normal is 0.11%, but 39% in the tumor. This could be due to a tumor contamination of the normal control.

ADD REPLYlink written 8 days ago by ATPoint3.0k

That's a good point. Although I would expect that if contamination happens it's the other way around. But we don't know how the samples were collected and which type of tumor is studied.

ADD REPLYlink written 8 days ago by WouterDeCoster26k

It is a lymphoma sample so probably tumor is a lymph node biopsy, and normal is PBMC . Would not be too uncommon if some malignant B cells escaped the lymphatic system and started circulating.

ADD REPLYlink modified 8 days ago • written 8 days ago by ATPoint3.0k

Right, sounds reasonable.

ADD REPLYlink written 8 days ago by WouterDeCoster26k

Yes the sounds reasonable, I have to check the settings in varscan. Probably I have to allow to define Germaine above a percentage or number of reads. Any suggestions?

ADD REPLYlink written 8 days ago by fabbri.marco0

There is the --max-normal-freq flag in ./VarScan2 processSomatic, default is 0.05 so 5% as maximum frequency for normals. Did you reduce that to 1%? If so, try with the defaults. I think this makes biological sense to exactly exclude these kinds of situations you experience right now.

ADD REPLYlink written 8 days ago by ATPoint3.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1208 users visited in the last hour