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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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a bam file contains single-end and paired-end reads #113

Open lancer-lu opened 4 years ago

lancer-lu commented 4 years ago

**Hi, I'm confused about the option: --bam/--jumps/--frags/unpaired. When my bam file contains single-end and paired-end reads, which option should I choose?

In the beginning, my reads is paired. I merged the paired-end reads to better identify the species when analyzing metagenome data, but part of the reads can't merge , so the bam file contains single-end and paired-end reads.

 I am looking forward to your reply, thank you!**
SergejN commented 4 years ago

I had a similar issue and ended up splitting the BAM files into those that only contain paired-end reads and those that contain single-end reads. Then you can supply the former with --frags and the latter with --unpaired. This is very unpractical for large BAM files, though, therefore, currently I run the mapper twice for paired and unpaired reads.