YFitter

Yfitter is a program for assigning Y chromosome haplogroups to individuals sequenced at low coverage. It is designed to be used in a samtools/bcftools pipeline. Yfitter also supports haplogrouping using chip genotype data.

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License

GNU General Public License version 3.0 (GPLv3)

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federete Posted 2016-04-27

Nice tool! However it is a bit tricky to make it work. This is how I managed to do with advice from the developer of the tool. First, extract the Y chromosome from the input bam (we don't need the other chromosomes). Use a recent version of samtools, like 1.2: samtools view -hb input_bam Y > chrY.bam Then, make a bcf file. You need an older version of samtools [version 0.1.19]: samtools mpileup -gf path_to/human_genome.fasta chrY.bam > chrY.bcf Then, again with version 0.1.19, get the genotype likelihoods for the interesting sites (karafet): bcftools view -Q -l karafet_sites_b37.pos chrY.bcf > chrY.qcall Finally, run Yfitter: Yfitter -m karafet_tree_b37.xml chrY.qcall > results.YFit

Additional Project Details

Intended Audience

Science/Research

Programming Language

C++, Python

Related Categories

Python Bio-Informatics Software, C++ Bio-Informatics Software

Registered

2011-06-23

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