RealignerTargetCreator GATK alignment

Question

[mailfromiob]

Please guide me, what is the difference between the two vcf files 1000G_phase1.indels.chrb37.vcf and Mills_and_1000G_gold_standard.indels.chrb37.sites.vcf?

Answer 1

[rbagnall]

Mills_and_1000G_gold_standard.indels.b37.sites.vcf is an indels dataset that was created at the Broad by strictly curating the Mills et al Genome Research, 2011 (PMID: 21460062) dataset.

1000G_phase1.indels.b37.vcf are very high confidence indels currently from the 1000 Genomes Phase I indel calls.