Questions tagged [htslib]
The htslib tag has no usage guidance.
12
questions
1
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1
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Reading same BAM file twice with htslib
I would like to read iteratively the same BAM file twice using htslib.
My option is to use hts_open, ...
- 113
1
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2
answers
345
views
Can HTSlib extract bam reads occurring in a specific region without iterating through the whole file?
I am using htslib/sam.h to write a C++ program. As part of this program, I must extract reads occurring on specific scaffolds in specific regions from a bam file. Essentially, I want to perform the ...
- 189
2
votes
1
answer
151
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How do I access sequence and MAPQ from bam using HTSlib in C++?
I am using the "htslib/sam.h" header in C++. I need to access the SEQ field of bam reads and store each sequence in a vector of strings. I also need to access the MAPQ field of each read to ...
- 189
3
votes
1
answer
230
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Use Htslib to extract specific region of vcf file
I am working in c++ using the htslib library to parse different vcf files as well as fasta files.
My goal is to read in a specific region from a fastafile and then extract all the VCF sites within ...
- 85
0
votes
1
answer
890
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extract chimeric and multimap reads from bam file
I am trying to extract all chimeric and multi-map reads from either SAM/BAM file. Is there any simple command to do that? Can I use htslib for parsing sam/bam files ...
- 195
1
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1
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131
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How to print alternative allele from VCF with htslib c++
I would like to print the alternative allele from a vcf file which i load in with htslib.
The description of some functions:
https://github.com/samtools/htslib/blob/develop/htslib/vcf.h
I have used ...
- 85
1
vote
0
answers
313
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How to troubleshoot access to tabix file via http or https?
I have some BED files that I have compressed with bgzip and indexed with tabix.
I am using version ...
- 3,125
2
votes
1
answer
144
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SAM format: Does the BAM "Integer or numeric array" field no longer exist? Why?
The SAM file format specification makes clear that optional fields must follow the format TAG:TYPE:VALUE
...
- 1,403
7
votes
2
answers
645
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How does htslib/samtools access optional BAM fields?
I am confused regarding how various software libraries deal with optional fields in a BAM:
Based upon the BAM specification, there are 11 mandatory fields to a BAM:
...
- 1,403
3
votes
1
answer
769
views
How to use C++ htslib to read VCF contig name and size?
A typical VCF file has:
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
I would like to use ...
- 2,739
5
votes
2
answers
2k
views
bcftools output vs. bgzip
I've got what seems like it should be a simple question, but I can't seem to figure it out from google. bcftools has 4 output options:
...
- 1,816
13
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1
answer
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What's the difference between VCF spec versions 4.1 and 4.2?
What are the key differences between VCF versions 4.1 and 4.2?
It looks like v4.3 contains a changelog (specs available here) but earlier specifications do not.
This biostar post points out one ...
- 366