Question: select Het variants from VCF
0
gravatar for zengtony743
2.3 years ago by
zengtony74370
Canada
zengtony74370 wrote:

I am trying to select heterozygotes from the VCF file. having been using this command many times and it works all the time. But something error pops up this time, do not know what is the problem.

1) partial data line information is like this

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 4751_42R

chr10 3101362 rs33880920 G C 189.60 . ABHom=1.00;AC=0;
AF=0.00;AN=0;BaseQRankSum=0.742;DB;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000
;MQ=57.19;MQ0=0;MQRankSum=-0.742;QD=31.60;ReadPosRankSum=0.742 GT ./.
chr10 3101529 rs29314734 C T 116.56 . ABHet=0.500;ABHo
m=0.933;AC=0;AF=0.00;AN=0;BaseQRankSum=-0.212;DB;DP=14;Dels=0.00;FS=5.332;Haplot
ypeScore=0.0000;MQ=60.00;MQ0=0;MQRankSum=0.000;OND=0.056;QD=16.65;ReadPosRankSum
=-0.271 GT ./.

2)

$ java -Xmx20g -jar /hpf/tools/centos6/gatk/3.6.0/GenomeAnalysisTK.jar -T SelectVariants -R genome.fa --variant 4751_42map.vcf -select 'vc.getGenotype("4751_42R”).isHet()' -o 4751_42maph.vcf

3)

Error is
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Argument select-0has a bad value. Invalid expression used (vc.getGenotype("4751_42R”).isHet()). Please see the JEXL docs for correct syntax.
ERROR ------------------------------------------------------------------------------------------
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by zengtony74370
1
gravatar for zengtony743
2.3 years ago by
zengtony74370
Canada
zengtony74370 wrote:

finally figured it out...

because of "4751_42R” should be

"4751_42"

ADD COMMENTlink written 2.3 years ago by zengtony74370

why ?? it's 4751_42R in the vcf header...

ADD REPLYlink written 2.3 years ago by Pierre Lindenbaum114k

Sorry for the typo. I mean it should be "4751_42R" but not "4751_42R” the keyboard for the new Macbook is so confusing

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by zengtony74370
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