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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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Bio-InformaticsLicense
GNU General Public License version 3.0 (GPLv3)Follow YFitter
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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