gender mask bed file vs gender map file
traceyc
Member ✭
Hi,
In the documentation for SVPreprocess (http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_SVPreprocess.html), there is an advanced parameter -genderMaskBedFile, but in the install test and another documentation page for SVPreprocess (http://gatkforums.broadinstitute.org/discussion/1514/svpreprocess-queue-script), there is a parameter -genderMapFile listed, but no -genderMaskBedFile. Is the difference related to software version or something else? I may be misunderstanding the functions of these parameters and their appropriate files, but if I know the genders of the samples I'm using and specify a genderMapFile, then I do not need to specify a genderMaskBedFile, which would be used to estimate sample gender?
Thanks,
Tracey
Best Answer
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bhandsaker
admin
They are different parameters with different purposes.
-genderMapFile is a way to provide the gender of each sample in your input data set.
In newer versions of Genome STRiP, we do gender estimation during preprocessing and by default we will use the called gender in downstream calling (at least in the CNV pipeline). The automated gender calling results are in metadata/sample_gender.report.txt and metadata/chrY_vs_chrX.pdf. You can override these if you want using -genderMapFile.-genderMaskBedFile is a file used to mask certain regions of the sex chromosomes to get better results in the automated calling described above. This mask depends on the reference genome and is part of the reference metadata bundle.
Answers
They are different parameters with different purposes.
-genderMapFile is a way to provide the gender of each sample in your input data set.
In newer versions of Genome STRiP, we do gender estimation during preprocessing and by default we will use the called gender in downstream calling (at least in the CNV pipeline). The automated gender calling results are in metadata/sample_gender.report.txt and metadata/chrY_vs_chrX.pdf. You can override these if you want using -genderMapFile.
-genderMaskBedFile is a file used to mask certain regions of the sex chromosomes to get better results in the automated calling described above. This mask depends on the reference genome and is part of the reference metadata bundle.