Compare the samples in a VCF

Question

[marzieh]

I have a VCF file that contains several samples. I want to compare them in the observed variation (snp or indel) with the reference genome and find out the difference between each sample with the reference genome and other samples. Thank you for your help.

Answer 1

[Pierre Lindenbaum]

let's run GenotypeConcordance https://gatk.broadinstitute.org/hc/en-us/articles/360037425091-GenotypeConcordance-Picard- for each pair of samples in the VCF using nextflow+DSL2.

invoke:

$ nextflow run biostar9524046.nf -resume --vcf /path/to/rotavirus_rf.vcf.gz
N E X T F L O W  ~  version 21.10.1
Launching `biostar9524046.nf` [prickly_engelbart] - revision: beae5906d6
[d6/a2709f] Cached process > downloadPicard
[fa/dd52d5] Cached process > vcf2samples (rotavirus_rf.vcf.gz)
[96/159978] Submitted process > concordance (S2 / S1)
[60/5b6c6c] Submitted process > concordance (S1 / S2)
[2b/ef2d1a] Submitted process > concordance (S3 / S1)
[44/852213] Submitted process > concordance (S3 / S2)
[db/75d074] Submitted process > concordance (S1 / S3)
[82/7e4a04] Submitted process > concordance (S2 / S3)
[d7/0b8a83] Submitted process > concordance (S4 / S1)
[30/9cfd01] Submitted process > concordance (S4 / S2)
[d7/3a3a25] Submitted process > concordance (S4 / S3)
[b5/ee4116] Submitted process > concordance (S1 / S4)
[26/45f653] Submitted process > concordance (S2 / S4)
[17/d0d9ce] Submitted process > concordance (S3 / S4)
[12/1e0366] Submitted process > concordance (S5 / S1)
[ce/e29a79] Submitted process > concordance (S5 / S2)
[e9/4c1aef] Submitted process > concordance (S5 / S3)
[c5/729b74] Submitted process > concordance (S5 / S4)
[65/15bd00] Submitted process > concordance (S1 / S5)
[97/278278] Submitted process > concordance (S2 / S5)
[e0/4d4a09] Submitted process > concordance (S3 / S5)
[d4/b65de3] Submitted process > concordance (S4 / S5)
[34/5aea8d] Submitted process > zipIt (N=20)

$ unzip -l work/34/5aea8d72432b32b03bf7870685eb87/concordances.zip  | head
Archive:  work/34/5aea8d72432b32b03bf7870685eb87/concordances.zip
  Length      Date    Time    Name
---------  ---------- -----   ----
     1102  05-21-2022 16:22   S2_S1.genotype_concordance_detail_metrics
     1124  05-21-2022 16:22   S2_S1.genotype_concordance_summary_metrics
      968  05-21-2022 16:22   S2_S1.genotype_concordance_contingency_metrics
     1126  05-21-2022 16:22   S1_S2.genotype_concordance_summary_metrics
      968  05-21-2022 16:22   S1_S2.genotype_concordance_contingency_metrics
     1102  05-21-2022 16:22   S1_S2.genotype_concordance_detail_metrics
      968  05-21-2022 16:22   S3_S1.genotype_concordance_contingency_metrics