How to extract all the IDs of VCF file for GWAS analyses?

Question

[Qingyang Xiao]

Hi,

How can I extract the genotyped ID out of the VCF file?

I need to select a subset of samples for GWAS analyses.

Thanks!

[Kevin Blighe]

How to extract info of samples of interest from VCF file?

[Qingyang Xiao]

Hi Kevin,

The problem is slightly different. Here I only want the list IDs, not VCF file containing information of a subset of IDs.

Some simple way to extract all IDs? Thanks!

[Pierre Lindenbaum]

what do you mean with ID ? ID is the 3rd column of the VCF.

Answer 1

[Kevin Blighe]

Take a look:

bcftools view -h Merge.UnFiltered.TumorOnly.vcf.gz | tail -1 ;
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  1174-N  1174-T  1292_CD19-T 1292_noCD19-N   1299-N  1299-T  1347-N  1347-T1378-N    1378-T  1584-N  1584-T  1696-N  1696-T  1700-N  1700-T  1823-N  1823-T  2111-N  2111-T  2217-N  2217-T  2297_CD19-T 2297_noCD19-N   2327_CD19-T 2327_noCD19-N   2343-N  2343-T  2474-N  2474-T  2514-N  2514-T  2530-N  2530-T  2584-N  2584-T  2596_CD19-T 2596_noCD19-N   2623-N  2623-T2822-N    2822-T  2896-N  2896-T  2925-N  2925-T  2946_CD19-T 2946_noCD19-N   2983-N  2983-T  2994-N  2994-T  3034_CD19-T 3034_noCD19-N   3053-N3053-T    3068-N  3068-T  3112-N  3112-T  3146_CD19-T 3146_noCD19-N   3239-N  3239-T  3252-N  3252-T  3396-N  3396-T  3453-N  3453-T  3498-N  3498-T3505-N    3505-T  3520_CD19-T 3520_noCD19-N   3540-N  3540-T  3583-N  3583-T  3592-N  3592-T  3597-N  3597-T  3764-N  3764-T  3819-N  3819-T  3833-N3833-T    3926-N  3926-T  3929-N  3929-T  3953-N  3953-T  4000_CD19-T 4000_noCD19-N   4054-N  4054-T  4074-N  4074-T  4090_CD19-T 4090_noCD19-N4119-N 4119-T  4152-N  4152-T

..or:

bcftools view -h Merge.UnFiltered.TumorOnly.vcf.gz | tail -1 |\
  awk -F "\t" '{for (i=1; i<=NF; i++) {if (i>9) {print $(i)}}}' ;
1174-N
1174-T
1292_CD19-T
1292_noCD19-N
1299-N
1299-T
1347-N
1347-T
1378-N
1378-T
1584-N
1584-T
1696-N
1696-T
1700-N
1700-T
1823-N
1823-T
2111-N
2111-T
...

...or:

bcftools view -h Merge.UnFiltered.TumorOnly.vcf.gz | tail -1 |\
  sed 's/\t/\n/g' | sed '1,9d' ;
1174-N
1174-T
1292_CD19-T
1292_noCD19-N
1299-N
1299-T
1347-N
1347-T
1378-N
1378-T
1584-N
1584-T
1696-N
1696-T
1700-N
1700-T
1823-N
1823-T
2111-N
2111-T
...

Kevin

[Pierre Lindenbaum]

or

bcftools query -l in.vcf

[Kevin Blighe]

En effet, Monsieur.