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about the use of varscan, somaticsnipper and samtools

Dear all,

please could you advise : before the use of eitther varscan, somaticsnipper or samtools to call the somatic mutations, would we need to :

a, mark the duplicates b. realign the data around indels (as we would do typically with GATK, before running Mutect) ?

many thanks !

bogdan

sequencing snp
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written by Bogdan Bogdan

3 answers

a) yes, mark duplicates in your bam files

b) no, local indel realignment is not necessary

c) I wouldn't rely solely on somatic sniper or varscan for detecting indels. They'll provide some useful information, but Pindel-C and GATK generally perform better on indel calling.

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written by Chris Miller Chris Miller

Hi Chris, Can you elaborate on why you say that local indel realignment is not necessary? Is it that you see no benefit, or that some callers do not need the local realignment preprocessing in order to deal with non-canonical alignments? Our (RTG) somatic caller internally does something similar to local realignment to candidate haplotypes when calling complex regions such as indels or dense snps, so realignment is not needed as a separate preprocessing step, and I imagine that callers incorporating local assembly also do not need realignment preprocessing.

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written by Len Trigg Len Trigg

Definitely the latter. I can't comment on whether there is any benefit, but the specific tools he mentioned do not require it.

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written by Chris Miller Chris Miller

Thanks Chris ! Talking about somatic variant calling, which one of these 4 would you recommend : STRELKA, MUTECT, VARSCAN or SOMATICSNIPPER ? Or perhaps some other somatic variant caller ?

what about the SV detection or CNV ? Any recommendation is welcome ! many thanks !

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written by Bogdan Bogdan

Chris, thank you very much !

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written by Bogdan Bogdan

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