BOL: Question: error: mate does not occur next to it in your BAM file. How to fix it ?

Question: Question: error: mate does not occur next to it in your BAM file. How to fix it ?

biogeek
1459 days ago

Question: error: mate does not occur next to it in your BAM file. How to fix it ?

*****WARNING: Query v300043428L4C001R0481272249 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.

Answers

Filter the suplementary alignments

samtools view -F 2048 -bo out.bam in.bam

Then try, it should fix the error.

Jit 1438 days ago