How to delect lines from BAM? using manual input index

Question

[wt215]

I have 2 BAMs of the some reads, but mapped to different genome. I extracted MAPQ from both, and get some index which correspond to reads that have the same MAPQ in both BAMs (using R). Then I can export those index in txt format.

Now how do I use the index found, for example, 2,3,4,5,8,9, to subset one of the BAM file?

The real problem is a bit more complex, as there are more than 2 BAMs, and I need to summarize the MAPQ across them.

Many thanks!

Answer 1

[wt215]

Found a solution here (https://bioinformatics.stackexchange.com/questions/3380/how-to-subset-a-bam-by-a-list-of-qnames): samtools view file.bam | grep -f 'qnames.txt > subset.sam

The frustrated thing is, it seems that after filtering the BAM, in 10X, you have to convert it back to fastq then rerun the analysis.