VariantFiltration for non-human data
Posted in Ask the GATK team | Last updated on 2012-10-29 22:02:53


Comments (3)

Hi all,

I'm currently analysing non-human mammalian whole genome data (>30x). No previous variants databases are available.

I'm currently in the VariantFiltration step. I came around the following command which is used for human data, and I'm wondering if it will be good for non-human data:

java -Xmx10g -jar GenomeAnalysisTK.jar \
-R [reference.fasta] \
-T VariantFiltration \
--variant [input.recalibrated.vcf] \
-o [recalibrated.filtered.vcf] \
--clusterWindowSize 10 \
--filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \
--filterName "HARD_TO_VALIDATE" \
--filterExpression "DP < 5 " \
--filterName "LowCoverage" \
--filterExpression "QUAL < 30.0 " \
--filterName "VeryLowQual" \
--filterExpression "QUAL > 30.0 && QUAL < 50.0 " \
--filterName "LowQual" \
--filterExpression "QD < 1.5 " \
--filterName "LowQD" \
--filterExpression "SB > -10.0 " \
--filterName "StrandBias"

I would appreciate your thoughts on this matter.

Thank you very much!

Sagi


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