Tagged with #targetcoverageefficiency
0 documentation articles | 0 announcements | 1 forum discussion

No articles to display.

No articles to display.

Created 2015-01-12 10:10:49 | Updated 2015-01-12 10:56:11 | Tags: targetcoverageefficiency multi-sample variant-calling merge-bam

Comments (8)

Hi, I have with me 1000 samples that were pooled together in 5 different libraries and sequenced for genomic regions. So first, for each library, I independantly performed alignment, marked duplicates,realigned the bam files and also did recalibration and separated the bam file for each individual. Now I have 1000 individual bam files and I wanted to check the target coverage and perform variant calling. I wanted to know if it makes sense to merge the bam files according to cases:controls and perform the analysis with 2 bam files or is it better to carry on with single individual bam files ?

Many thanks.