Hello,all
while using the walker PhaseByTransmission I always get this error:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.1-12-ga99c19d):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: File associated with name java.io.FileReader@5cf7c5b5 is malformed: Bad PED line 1: wrong number of fields
##### ERROR ------------------------------------------------------------------------------------------
my conmmand is :
java -jar GenomeAnalysisTK-2.1-12-ga99c19d/GenomeAnalysisTK.jar -T PhaseByTransmission -R GRCh37.fasta -V trios_457.chr22.vcf -ped trios_457.chr22.ped -pedValidationType SILENT -o o1.vcf
and my ped file is like this:
fam1 s_4 0 0 1 1 C C C C G G
fam1 s_5 0 0 2 2 T T T T G G
fam1 s_7 s_4 s_5 2 2 C T C T G G
I do counted my vcf ped and map files and the result is:
-bash-4.1$ head -1 trios_457.chr22.ped |wc -w
1892 #( 6 columns for info + 943*2 columns for alleles )
-bash-4.1$ wc -l trios_457.chr22.map
943
-bash-4.1$ grep -v "#" trios_457.chr22.vcf | wc -l
943
My question is what's wrong with my my PED line?