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walaj / svaba

Structural variation and indel detection by local assembly
GNU General Public License v3.0
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How to input multiple case bams? #118

Closed kimin0402 closed 2 years ago

kimin0402 commented 2 years ago

Hi, just a quick question

From the instruction of svaba, it says more than 1 bam file can be given as input for case bam.

I tried to call somatic SV in multiple bam files with one control bam, so the code was like the following

$svaba run -t tumor1.bam,tumor2.bam,tumor3.bam -n normal.bam

But svaba throws error. I tried spaced separated, comma separated list of bams, but it didn't work.

How can I fix this?

walaj commented 2 years ago

Each gets its own -t flag. The idea of the multiple bams in one run is if they are related samples -- e.g. trios or multiple tumors from the same patient. I would not use this from unrelated tumors or patients. The results will be combined across all, and the genotype field will indicate which files have the variant supporting reads.