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v0.14 implemented both inherited variant calling and de novo mutation detection from VCF input files. If you have a VCF file with PL or GL fields, you can run polymutt on the VCF file to quickly and conveniently call variant and mutations.
v0.14 implemented both inherited variant calling and de novo mutation detection from VCF input files. If you have a VCF file with PL or GL fields, you can run polymutt on the VCF file to quickly and conveniently call variant and mutations.
*NOTE: When there is missing data in a trio or family, the de novo calling is not reliable and often times is not possible. So these sites should be ignored for de novo mutations.
v0.13 fixed the bug for generating genotypes when the input is a VCF file and the ped file contains only a single nuclear family. Like unrelated samples (e.g. [[http://gatkforums.broadinstitute.org/discussion/1186/best-practice-variant-detection-with-the-gatk-v4-for-release-2-0 GATK]] recommends at least 30 samples), it is also desirable to use more families or mixture of families and unrelated samples for polymutt.
v0.13 fixed the bug for generating genotypes when the input is a VCF file and the ped file contains only a single nuclear family. Like unrelated samples (e.g. [[http://gatkforums.broadinstitute.org/discussion/1186/best-practice-variant-detection-with-the-gatk-v4-for-release-2-0 GATK]] recommends at least 30 samples), it is also desirable to use more families or mixture of families and unrelated samples for polymutt.
