Read groups in SAM file header

amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

https://www.microsoft.com/en-us/research/project/snap/

Apache License 2.0

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Read groups in SAM file header #3

Closed rnpandya closed 9 years ago

rnpandya commented 12 years ago

From Ilya Chorny ichorny@gmail.com

SAM/BAM file test.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups

antunderwood commented 12 years ago

bolosky commented 12 years ago

I added a very simple read group. I'm going to leave the issue open, because SNAP should both be able to take input as to what should go in the read group as well as copying the information when the reads come from a SAM file rather than FASTQ.

bolosky commented 9 years ago

It can take read groups specified on the command line, or copy them from a SAM/BAM input. This has also been true for years.