Hello, I have the following line of code: ``` /Plink1.9/plink --bfile "${PLINK_REF_PANEL}/${chrom}".final \ --r2 \ --ld-window 10000 \ --ld-window-r2 ${PLINK_MIN_R2} \ --keep "${PLINK_REF_PANEL_KEEP}" \ --out …

I'm looking for help understanding the example of spanning alleles and multi-allelic loci on https://luntergroup.github.io/octopus/docs/guides/advanced/vcf/ The ALT field values are OK, but the GT values …

Hey everyone, I am trying to split the multiallelic sites of my VCF. I used `bcftools norm --m-any`. However, the result is not really reasonable …

The BIM file from PLINK contains the variant information that accompanies a BED file. The variants called are based on exome sequencing. However, I encounter …

I have a plink (bed, bim, fam) file. The .bim file has chr strings and I would like to remove chr. Is there any inherent …

I am trying to sync up bim files from two different builds so that they have the same position and rsid for each variant I …

I got a PLINK file from a publication. I want to have the major allele correspond to the forward strand of hg19 because I want …

Hello, I am trying to update rsids then chromosome # in a PLINK file .bim file starts out looking like this: 23 23:2700157:G:A 0 2700157 …

I have downloaded the 1000 genomes dataset from http://hgdownload.cse.ucsc.edu/gbdb/hg19/1000Genomes/phase3/ I have converted it to bgzip format, and am doing some QC using bcftools. I have …

Hi, I have *plink* files with SNPs annotated like `"exm"` or with chromosomal position followed by the rsID, 6:33960611:rs2495990 0 33960611 A G 6:33962404:rs2130410 0 …