SHAPEIT involves at the least four columns in the SAMPLE file. Additional columns could be extra but SHAPEIT will dismiss them. This file must have N+one strains and at least four columns in which N will be the selection of individuals from the reference panel.
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* Slight: When running on ped/map documents at monomorphic SNPs the output information detailed The 2 alleles as the noticed allele and 0.This has now been improved so the noticed allele is detailed 2 times.This gives far better compatibility with IMPUTE2.
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And glitches when someone or possibly a web-site has a lacking facts rate of a hundred%. have a peek here Moreover, SHAPEIT generates two extra log files to aid the detection of any issues check during the input knowledge.
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The 2nd presents absolutely the route of the BAM file. This fundamentally tells to extractPIRs in which the BAM file is physically located on the computer.
The primary column presents the sample ID comparable to the BAM file. This sample ID has got to match among the list of sample ID while in the VCF to ensure that extractPIRs to correctly map sequencing reads to samples.
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