Hi all and hopefully Dan,
I am still not very sure about how to use the Varscan2 filters for SNVs and Indels obtained. Below are my questions, any advice on the clarification of using the filters will be appreciated.
1) For a single sample,
Step 1. Use pileup2snp and pileup2indel call SNVs and Indels.
Step2. Run varscan2 filter on SNVs using the Indels as an input. Then filter indels using java -jar varscan2 filter output.indel >filtered.indel.
Aternatively,
Step2. Another option is to filter indel first and use the filtered indels as input to filter SNVs.
Which one is better for step 2?
2) For a Normal/Tumor sample,
From the context of the Varscan2 instruction, the "somaticFilter" is designed only for filtering SNVs, not for indels. So there is actually no filter for Indels. The Indel file obtained from calling Varscan2 somatic will be the final reported Indel. Is that correct? Is somaticFilter applicable to Indels?
Of course, we can change any somatic indel with read2>0 into Germline.
Thank you all!
I am still not very sure about how to use the Varscan2 filters for SNVs and Indels obtained. Below are my questions, any advice on the clarification of using the filters will be appreciated.
1) For a single sample,
Step 1. Use pileup2snp and pileup2indel call SNVs and Indels.
Step2. Run varscan2 filter on SNVs using the Indels as an input. Then filter indels using java -jar varscan2 filter output.indel >filtered.indel.
Aternatively,
Step2. Another option is to filter indel first and use the filtered indels as input to filter SNVs.
Which one is better for step 2?
2) For a Normal/Tumor sample,
From the context of the Varscan2 instruction, the "somaticFilter" is designed only for filtering SNVs, not for indels. So there is actually no filter for Indels. The Indel file obtained from calling Varscan2 somatic will be the final reported Indel. Is that correct? Is somaticFilter applicable to Indels?
Of course, we can change any somatic indel with read2>0 into Germline.
Thank you all!
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