Estimation of normal/tumor pairs contamination using Conpair - Compatibility with GATK4
Hi I have normal/tumor BAM files and I am trying to estimate contamination using Conpair. I managed to tun Conpair before with GATK3.8 but not my system is updated and I am not able to make Conpair work with GATK4. I wonder if anybody else also faced this problem and managed to resolve it.
Command:
python3 /DATA/General_Resources/Tools/Conpair/scripts/run_gatk_pileup_for_sample.py -B PRADO_data/7B_dedupraw/S2697Nr36_dedup.bam -O PRADO_data/NTmatch/S2697Nr36_pileup --reference /DATA/peeper_lab/reference_fasta_files/GRCh38.d1.vd1.fa /DATA/General_Resources/Tools/Conpair/data/markers/GRCh38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.liftover.bed --gatk /DATA/General_Resources/Tools/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar
Error:
A USER ERROR has occurred: '-T' is not a valid command.
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
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Pierre Lindenbaum
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Huma •
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Huma •
1 answer
the command lines syntax changed between gatk3 and gatk4.
you got something like
java -jar gatk.jar -T HaplotypeCaller -o out.vcf.gz ...
and now it's
gatk HaplotypeCaller -O out.vcf.gz ...
you cannot just 'swap' the two versions of gatk.
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Pierre Lindenbaum
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That seems to indicate an error on your part with the command line rather than system. I don't see a
-Tin your command so GATK seems to be unhappy about something in your command.