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Results tagged with samtools
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Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
4
votes
2
answers
655
views
What is a samtools mpileup reference skip?
The samtools documentation for mpileup states:
At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a '>' or '<' for a reference …
- 784
15
votes
1
answer
2k
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Are soft-clipped bases used for variant calling in samtools + bcftools?
If there are soft clipped base pairs specified in the CIGAR string for a read in a SAM/BAM file, will these be used for variant calling in a samtools + bcftools workflow? … The samtools documentation does not mention clipped bases. …
- 784
4
votes
2
answers
342
views
Filter bam using SNP list in bed format with minimum mapping quality and base quality
Samtools seems to almost solve this problem, but not quite:
samtools depth -b snp_list -q 20 -Q 30 example.bam allows me to count the number of alignments meeting my desired criteria, but not to produce … There is no -Q option for samtools view, and the -q option is for mapping quality
Can this be achieved in samtools? Or is there another preexisting tool that can? …
- 784
10
votes
1
answer
4k
views
What are all the reference files produced by bwa index, and are these dependent upon whether...
I have discovered that samtools does not take a gzipped reference, so I am planning to use an unzipped version of the reference for my workflow instead of dealing with two separate representations of the …
- 784