I have two bams with equivalent sams; one yields a validation error and the other does not.
Hi! I have two bam files whose sam equivalents are identical-- as in:
diff <(samtools view -h small.bam) <(samtools view -h smalltest.bam)
yields nothing, and when I run haplotype caller on one file I get errors that say (for every read):
Ignoring SAM validation error: ERROR: Record 1, Read name RSRS1, bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned
and no SNPs are generated, while the other file processes just fine.
Needless to say, the bin fields are the same.
To be clear, I generated one of the files, it generated the error, and when I converted from bam->sam->bam, GATK processed it correctly.
I'm using gatk-18.104.22.168, samtools verion 1.7 (htslib 1.9)