is needed info (BAM and MAF) files for normal tissues in MUSIC?

Question

[Marina Manrique]

Hi there!

I'm thinking about using MUSIC on a set of cancer samples but I don't have data for normal tissue. Could I use MUSIC with info of only tumor tissues?

Thanks,

Marina

[hengtaofly]

Hi,Cyriac:

According to your vcf2maf.pl script, it need VEP annotation for the vcf files, could I use the results genetated by annovar instead of using VEP?

Looking forward to your reply,thanks!

Hengtao

[Cyriac Kandoth]

No. It only works with VEP. In the future, please ask a new question on biostars.

[hengtaofly]

Thank you very much, i will remember that~

Answer 1

[Cyriac Kandoth]

Yes, you can. When using music calc-covg, you can use the tumor BAM as both tumor/normal, since it's only used to measure sequencing coverage. For the MAF, you need to be careful about recurrent false-positives, especially germline mutations. There are many strategies to filter out sufficiently common germline calls, if you don't have matched normal tissue per tumor. For example, you can use the maf2maf script to generate a new MAF with VEP annotations, and then filter out sufficiently common SNPs/Indels at >0.05% minor allele freq in any EVS/1000G cohort:

perl -a -F'\t' -ne '$cm=0; map{($al,$fr)=split(/:/); $cm++ if($fr>0.0005)}@F[76..82]; print if($cm<1)' input.vep.maf > input.vep.filtered.maf

[Marina Manrique]

Thanks a lot Cyriac for the quick reply.

Cheers!

marina