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Would anybody happen to know a link to where I can download BCF Tools?
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If you mean Heng Li's software, they are part of the latest samtools distribution, see
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Ah! thank you, epigen!!!Comment
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was wondering what is the command to use bcftools if it is installed as a part of samtools, pleaseOriginally posted by JohnK View PostComment
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If it is installed on your computer, typing bcftools at the commandline prompt should give you something like this:
Otherwise, have a look in the samtools directory, there should be a subdirectory called bcftools.Code:$ bcftools Program: bcftools (Tools for data in the VCF/BCF formats) Version: 0.1.17-dev (r973:277) Usage: bcftools <command> <arguments> Command: view print, extract, convert and call SNPs from BCF index index BCF cat concatenate BCFs ld compute all-pair r^2 ldpair compute r^2 between requested pairsComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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