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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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exclude secondary alignment and have mapq cutoff #26

Open ruolin opened 3 years ago

ruolin commented 3 years ago

Hi, it would be nice to exclude secondary alignment by default. Thanks.

PengJia6 commented 3 years ago

@ruolin I think so, but do you have any supporting evidence? And what about the supplementary alignment? Thanks!

ruolin commented 3 years ago

Thanks for the quick response. I know user can filter the bam first. But it is an extra step. It is good to exclude supplementary too. Those reads are inflating the counts. For example, you can take a look at region chr1:44,227,913-44,227,953 on HG19. I used NA12878. Although it is our in-house data, any public NA12878 would prove my point too, I assume.

PengJia6 commented 3 years ago

@ruolin Thanks for your suggestions, I will check it and update in next release!

ruolin commented 3 years ago

Thanks!