HaplotypeCallerSpark
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20 months ago
quentin54520 ▴ 90

Hello all,

I try to use gatk haplotypecallerspark. I have gatk 4.2.0.0. My data are human WGS (40X). Each bam is arround 100 Go. I try this command, but it stops less than 2 minutes after begining (i don't see what is the error in the log file, or at least i didn't understand) :

gatk --java-options "-Xmx40G" HaplotypeCallerSpark \
-R /Path/ref.fa \
-I /path/input.bam \
-O /path/output.g.vcf \
-ERC GVCF \
--tmp-dir /path/tmp \
-- \
--spark-master local[10]

Someone have an idea of how i can use haplotypecaller? If i use the non spark haplotypecaller it will be very long? I have 74 WGS.

If you want to see the log file it's here

Thank's in advance,

Quentin

Variant gatk haplotypecaller • 1.3k views
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I changed.

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you should post this log file to the gatk forum.

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Did you find any solution? This same happens while using ApplyBQSRSpark tool of GATK

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