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2 hours ago by

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gatk  -T CalculateGenotypePosteriors 
 -R $reference 
 -V trio.cohort.vcf 
 -ped trio_cohort.ped 
 -supporting-callsets $gnomad 
 -o GP_triocohort.vcf

trio.cohort.vcf contains

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  001C1   001P1   001P2   001c2   003C    003P1   003P2   004C    004P1   004P2   007C    007P1   007P2   009C    009P1   009P2   010C    010P1   010P2   013C    013P1   013P2   022C    022P1   022P2   023C    023P1   023P2   030C    030P1   030P2   034C    034P1   034P2   036C    036P1   036P2   042C    042P1   042P2   044C    044P1   044P2

and trio_cohort.ped contains

#fam-id ind-id  pat-id  mat-id  sex phen
001     001C1   001P1   001P2    1  2
001     001c2   001P1   001P2    1  2
001     001P1   0         0      2  1
001     001P2   0         0      1  1
003     003C    003P1   003P2    1  2
003     003P1   0         0      2  1
003     003P2   0         0      1  1
004     004C    004P1   004P2    1  2
004     004P1   0         0      2  1
004     004P2   0         0      1  1
007     007C    007P1   007P2    1  2
007     007P1   0         0      2  1
007     007P2   0         0      1  1
....    ......      ..            ..         
044     044C    044P1   044P2    1  2
044     044P1   0         0      2  1
044     044P2   0         0      1  1

Getting the error as follows:

A USER ERROR has occurred: Invalid argument ' '.

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
genotype_posterior.sh: 7: genotype_posterior.sh: -ped: not found

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modified 2 hours ago

written
2 hours ago
by

dare_devil700



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