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I'm normally a C# / .net developer, but a new project is going to be working with Next Generation Sequencing BAM and VCF files. I will need to read these files, make some changes, and save them. As far as I can tell, there's not much in the way of existing .net libraries for working with these files.

What programming languages are typically used in this field, and have libraries supporting these files?

Timur Shtatland
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Kyle
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    java : htsjdk lib, C/C++ htslib, python: pysam, etc... for bioinformatics, you can ask: https://www.biostars.org/ – Pierre Feb 07 '20 at 08:02

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Python with pysam and pyvcf libraries. Or use shell with samtools, sambamba, vcflib, vcftools, bcftools and many other command line utilities. You can install many of them with bioconda.

Timur Shtatland
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