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



music bam maf • 2.1k views
ADD COMMENTlink modified 4.3 years ago by hengtaofly0 • written 5.9 years ago by Marina Manrique1.3k


According to your 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!


ADD REPLYlink written 4.3 years ago by hengtaofly0

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

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Cyriac Kandoth5.5k

Thank you very much, i will remember that~

ADD REPLYlink written 4.2 years ago by hengtaofly0
gravatar for Cyriac Kandoth
5.9 years ago by
Cyriac Kandoth5.5k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.5k 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 5.9 years ago by Cyriac Kandoth5.5k

Thanks a lot Cyriac for the quick reply. 



ADD REPLYlink written 5.8 years ago by Marina Manrique1.3k
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