1000G-retrieve-genotype-q2

Question

I would like to make a file with genotypes at specific loci for all individuals from the 1000G data with 3202 individuals (20201028_3202_raw_GT_with_annot). The positions should be common SNPs- snp151Common from UCSC, hg38. Select SNPs in which the observed allele column consists of exactly two distinct bases, where both alleles are strictly one of A, C, G, or T (i.e. not multi-allelic or indel). Further filter them to be within chr1 and within the 1000 genome-wide strongest peaks of the ENCODE peak file with accession ENCFF717TCQ (based on the qValue column). Create an uncompressed tsv with columns CHROM, POS, REF, ALT, and then the 3202 identifiers in lexicographic order (include header). In this tsv, the REF and ALT should come from the 1000G VCF. Keep those where both REF and ALT in 1000G are both exactly one of A,C,G,T. Convert any phased calls to unphased. Then, in the genotype cells, include only one of "0/0", "0/1", "1/1" or "./.", reserving "./." for any that were not exactly one of the first 3. The SNPs should be sorted by coordinate. Report the total number of lines in this file along with the md5sum of this file, in the format "201;md5sum".

Predicted answer

296;864b06501a76b44b3037072e25c99725Most likely answer for this question; not uniquely determined from submitted scores.

Domain

Population Genetics

Question style

Retrieval

An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.