Extracting participant level SNP dosage using BCPtool query

Bhawana Singh

I am looking to extract participant level SNP doasage for 1 variant using below bcptools command. However, it is returning file with 0kb. Can you please guide me why I am not getting any output? I have checked presence of this position in chr1 via bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\n' ukb24310_c1_b2753_v1.vcf.gz

bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[%tGT]\n' ukb24310_c1_b2753_v1.vcf.gz -r 1:55063542  -S list_of_samples.txt  -o Onesnp.tsv 

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    Bhawana Singh

    have resolved this, namung was chr1 and not 1

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