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SelectVariant from FILTER column

wukhanwukhan PakistanMember

Hi,

Dear GATK Team

I am wondering is there any option in GATK'S SelectVariants walker (I am quite sure that its the best as per my need) to select all those variants which have 'SnpCluster' record in the FILTER column. As I do not want those variants that have 'PASS' records.

I tried with this:
java -jar /home/wuk/software/GenomeAnalysisTK.jar -T SelectVariants -R /home/wuk/Working/gnme_refrnces/Homo_sapiens_assembly38.fasta -V snp_clsters2_ws3.vcf -o snp_clsters2_ws3_clstronly.vcf -select "FILTER == 'SnpCluster'"

and many other combinations but I failed every time. What should be the best walker option or JEXL argument for that?

Thanks,

Waqas.

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    Did this produce an error or just not the result you wanted?

    You might try dropping the single quotes from around SnpCluster, they shouldn't be necessary.

  • wukhanwukhan PakistanMember

    Yeah, you are right, so the correct command is:

    java -jar /home/wuk/software/GenomeAnalysisTK.jar -T SelectVariants -R /home/wuk/Working/gnme_refrnces/Homo_sapiens_assembly38.fasta -V snp_clsters2_ws3.vcf -o snp_clsters2_ws3_clstronly.vcf -select "FILTER == SnpCluster"

    Thanks,

    Waqas.

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