Closed jtarraga closed 7 years ago
To query by specific sample genotypes you can use --sample-genotype parameter. You must separate samples by ';', and the accepted genotypes for each sample by ','. This will execute an AND between samples and a OR for the genotypes, so in:
/build/bin/hpg-bigdata-local.sh variant query --i test.vcf.avro --sample-genotype "sample_index1:0/0;sample_index2:0/1,1/1"
variants which are 0/0 for sample index 1 and 0/1 or 1/1 for sample index 2 are returned
To query by specific sample genotypes you can use --sample-genotype parameter. You must separate samples by ';', and the accepted genotypes for each sample by ','. This will execute an AND between samples and a OR for the genotypes, so in:
/build/bin/hpg-bigdata-local.sh variant query --i test.vcf.avro --sample-genotype "sample_index1:0/0;sample_index2:0/1,1/1"
variants which are 0/0 for sample index 1 and 0/1 or 1/1 for sample index 2 are returned