vadimzalunin/crammer — Issue #20: Template length is off by 1
Author: vadimzalunin
Created: 2012-03-09 09:48:14+00:00
State: open

$ samtools view
NA12878.mapped.illumina.mosaik.CEU.exome.20110411.chr20.bam
20:64000-65000 | cut -f -9
SRR098401.102568768	147	20	63932	64	76M	=	63912	-95
SRR098401.7377046	99	20	63987	65	76M	=	64163	251
SRR098401.48777644	83	20	64005	65	76M	=	63864	-216
SRR098401.9345685	163	20	64010	56	76M	=	64099	164

$ samtools view
NA12878.mapped.illumina.mosaik.CEU.exome.20110411.chr20.bam.cram.bam
20:64000-65000 | cut -f -9
146	147	20	63932	64	76M	=	63912	-96
149	99	20	63987	65	76M	=	64163	252
144	83	20	64005	65	76M	=	63864	-217
151	163	20	64010	56	76M	=	64099	165

This comes from the Picard's routine but I'm not sure how to fix this and who is right.