Hello Biostar Friends, Reaching out to those with experience doing phasing especially with ShapeIt (current version ShapeIt5). Does anyone know what the best haplotype reference …

Hi, I have 3 vcf files and I want to merge these in the following format: #CHROM POS REF ALT-1 ALT-2 ALT-3 I used the …

Good afternoon, I have a problem regarding the generation of the index "number of haplotypes" on DnaSP6. I'm currently working on a sample made up …

I am working with 1000 Genome VCF files, it has a format like this : CHROM - POS - ID - REF - ALT - …

I am getting an error while using extractPIRs as follows ./extractPIRs --bam bamlist --vcf VCF.gz --out Reading genotypes in [/MOD_recalibrated_variants.vcf.gz] in VCF format * 477 …

Dear all, I have a problem at hand regarding the manipulation of multiple VCF files (containing the same variants and referred to the same sample) …

Is there any script or tool to Map gene SNP positions to genome coordinates, for example ``` CHROM POS ID REF ALT 1 60 . …

Hi all, Im trying to impute some genotype data on the Michigan imputation server (https://imputationserver.sph.umich.edu/ ). For autosomes this works perfect and straightforward. However for …

Hello Friends I have created vcf file for my samples using GATK. After variant calling i used snpEff for annotation. Now my vcf annotation files …

Hi all, I'm trying to use the SnpSift extractFields (SnpSift 4.1g (build 2015-05-17)) command to change a mpileup gVCF file into a nice tab delimited …