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Haplotypecaller: Problem with using ploidy argument.

nasimstnasimst Leuven, BelgiumMember

Dear GATK team,

I tried to fix the ploidy issue with sex chromosome in my pipeline, based on the information that I got from the previously asked questions.
However, when I run that, there is No difference in my output with -ploidy 1 and the default. I tried it also with nightly version but it did not work also.

My commands:

cmd="/usr/bin/time -a -v -o ${samplePrefix}.xy.timing java \
-Xmx10g -jar ${gatkPath}/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R ${refGenome} \
-I ${sampleInputPrefix}.${fileExt} \
--emitRefConfidence GVCF \
--variant_index_type LINEAR \
--variant_index_parameter 128000 \
--dbsnp ${dbSNPall} \
--sample_ploidy 1
-L ${targetxy} \
-o ${samplePrefix}.${build}.xy.HC.g.vcf.gz \
-nct ${threads} \
-log ${samplePrefix}.xy.log"



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