`LD_blocks.sh` is not functional

fgvieira / ngsLD

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

GNU General Public License v2.0

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`LD_blocks.sh` is not functional #37

Open cbird808 opened 2 years ago

cbird808 commented 2 years ago

ngsLD/scripts/LD_blocks.sh

The awk line assumes that the second column of a *.ld file has chom:pos info, but the second column has the major nucleotide of snp1. The fourth column (change $2 to $4) has the snp2 chrom:pos info. Then the subsequent cut needs to be updated to reflect the *.ld file format

fgvieira commented 1 year ago

Hi @cbird808

that script hasn't been used much and it might be outdated. Since it seems you have a pretty good idea of where the problems are, just submit a PR. best,