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roohy / iLASH

iLASH - IBD Estimation Using Locality Sensitive Hashing
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Error when running in multisample exome bcf #10

Open kvn95ss opened 1 year ago

kvn95ss commented 1 year ago

Hello,

We have a multisample bcf which was generated from a heterogenous exome data pool.

To generate the PED and MAP file, we used the command - time plink --bcf all_samples.bcf --recode tab --out outfile --double-id --allow-extra-chr

demo_idb was created using the test configuration, with the following modifications made - map outfile.map ped outfile.ped

But when we ran ilash demo_ibd we got the following error-

terminate called after throwing an instance of 'DimensionException' what(): The number of SNPs in at least one of the samples does not match the number of SNPs in the map file

However, we have not messed around with the output of plink! What could the issue be?

kvn95ss commented 1 year ago

Also, the missing genotypes were filled in as 0/0. The error still persists.

roohy commented 1 year ago

Hi, As the error suggests, there must be a problem with the number of SNPs in the map file. Firstly, I would check that the input file is phased. Secondly, I would check that the ped file is in the standard format. For example if missing genotypes are filled as 0/0 in the ped file, then it may not be standard since the alleles should be separated by a space and not a forward-slash. Additionally each allele should be represented by a single character in the file.