HaplotypeCallerSpark

Question

[quentin54520]

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

[Pierre Lindenbaum]

but it didn't work

https://meta.stackexchange.com/questions/147616

[quentin54520]

I changed.

[Pierre Lindenbaum]

you should post this log file to the gatk forum.

[Mansi]

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