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lh3
This is *NOT* the official repository of samtools.
Same issue as mentioned on the minimap2 tool: https://github.com/lh3/minimap2/issues/236#issue-361097444 For example nanopore reads aligned to the host transcriptome the flagstat output is: 5953480 + 0 in total (QC-passed reads +...
Region 536882283..536882433 cannot be stored in a bai index. Numerical result out of range But I need one bai file for next GATK calling snp for wheat WES data Is...
We are finding that when there is an ambiguity code in the reference (e.g an N), even if a base is called in the the mpileup step, that base is...
This avoids the following warning from uncompressed BAM files which don't end with the expected 28 byte empty BGZF block as an EOF marker: [bam_header_read] EOF marker is absent. The...
Dear samtools, I am working with FASTA alignments, which have different sequence names (aka chromosomes) but all of the same length. No I needed to create a wrapper around samtools...
HI, a BAM has their own MD tag and NM tag , why we need to recalculate MD/NM tags ? MD or NM from the origin bam is wrong ??...
I have a general question about AD\* counters. For some cases I get 2 counters, for other 3, or 4... look at the following example. For the first variant 3...
Dear Professor, It's very glad to meet you here! I have a question about Samtools faidx : what' the meanning of third and thirth and fifth cloumn in faidx result...