Make --SnpGap optionally filter also SNPs close to other variant types. (#1126) bcftools gtcheck: Complete revamp of the command. The new version is faster and allows N:M sample comparisons, not just 1:N or NxN comparisons. Some functionality was lost (plotting and clustering) but may be...
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=DN,Number=1,Type=String,Description="Possible values are 'Inherited', 'DeNovo' or 'LowDQ'. Threshold for passing de novo call: SNPs: 0.05, ...
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*-c, --collapse* 'snps'|'indels'|'both'|'all'|'some'|'none'|'id':: Controls how to treat records with duplicate positions and defines compatible records across multiple input files. Here by "compatible" we mean records which should be considered as identical by the tools. For example,...