Data can be imported in inPHAP in two different formats: The VCF file format containing haplotype information for different subjects as separated columns and the IMPUTE2 format, the default haplotype text file format used by the IMPUTE2 program [18] to encode genotype information from the 1000 ...
calling process is done independently for each haplotype, and variant calls are merged at the end in the order they are found in this table. To include a haplotype with no input, add an entry to a zero-byte file to make the haplotype appear in the merged variant table and in VCF ...
VariantFiltration : java –jar GenomeAnalysisTK –T VariantFiltration –R ref.fasta –V file_snps.vcf–filterExpression « QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < −12.5 || ReadPosRankSum < −8.0 » –filteredName «FILTER » -o filtered_s...
1 is a heterozygous at the raw variant; dipcall sets aGAP1filter if no >=50kb alignment from parent1 covers the variant. Note that if a call is covered by multiple >=50kb alignments in the same parent but the alignments all have the same allele, the call is not filtered in the VCF....
To confirm that the haplotype-resolved genome assemblies were correctly phased across all chromosomes, we independently assigned each 1-Mbp window of the assembled contigs to one of the two parents (that is, HG00731 and HG00732;Methods) by using a set of trio-phased SNVs produced earlier19....
whatshap compare --tsv-pairwise=eval.tsv truth.vcf phased.vcf 2. Inspect the output printed to the terminal or open the tab-separated value fileeval.tsvin a spreadsheet program (seeNotes 25and26). 4Notes 1. Because the average distance between variants in the human genome is on the order...