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brentp / duphold

don't get DUP'ed or DEL'ed by your putative SVs.
MIT License
100 stars 9 forks source link

--Sample name function can be useful #19

Closed idraktt closed 5 years ago

idraktt commented 5 years ago

Dear Brent,

First i want to say thank for that beatiful tool. We are implementing duphold filtration step in our cnv calling pipeline and it really helps to remove FPs. Unfortunately we came across with one issue when sample name in our snp vcf file is not the same as a SM tag in the BAM file. (Filename used for SAMPLE column in vcf file). Is it possible to add extra input parameter that will specify sample name to look for in snp vcf file?

brentp commented 5 years ago

I have just pushed a fix for this that allows the name to be set via the environment variable DUPHOLD_SAMPLE_NAME. This will be out in the next release.

Thanks for reporting.

idraktt commented 5 years ago

Thank you very much Brent for your help.

brentp commented 5 years ago

this is added, sorry for the long delay.