This is the default haplotype text file format employed by IMPUTE2 to encode the haplotypes in the one,000 Genomes Project. Exact facts in regards to the file format are available below.
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-T 8 This command line will likely have extactly exactly the same behaviour because the previous just one. Notice that in the rest of the documentation, We'll use this compact variety when attainable.
Test carefully the screen output plus the log file. The condition may be noted in this article considering that they equally comprise a lot of details about what is going on.
Note also that SHAPEIT haploid heterozygous as missing knowledge. On top of that, it generates two additional log information that help the person to spot any problems. If the most crucial log file is gwas.phased.log, they are:
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The next gives absolutely the route with the BAM file. This generally tells to extractPIRs where by the BAM file is bodily located on the pc.
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SHAPEIT needs at the very least 4 columns while in the SAMPLE file. Additional columns might be extra but SHAPEIT will ignore them. This file should have L+1 strains and at least 4 columns the place L is the number of SNPs from the reference panel. HAP file