Question: is needed info (BAM and MAF) files for normal tissues in MUSIC?
1
gravatar for Marina Manrique
2.7 years ago by
Marina Manrique1.3k
Granada
Marina Manrique1.3k wrote:

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

music bam maf • 1.1k views
ADD COMMENTlink modified 14 months ago by hengtaofly0 • written 2.7 years ago by Marina Manrique1.3k

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

ADD REPLYlink written 14 months ago by hengtaofly0

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

ADD REPLYlink modified 14 months ago • written 14 months ago by Cyriac Kandoth4.6k

Thank you very much, i will remember that~

ADD REPLYlink written 12 months ago by hengtaofly0
1
gravatar for Cyriac Kandoth
2.7 years ago by
Cyriac Kandoth4.6k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth4.6k wrote:

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 scriipt 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
ADD COMMENTlink written 2.7 years ago by Cyriac Kandoth4.6k

Thanks a lot Cyriac for the quick reply. 

Cheers!

marina

ADD REPLYlink written 2.7 years ago by Marina Manrique1.3k
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