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How to Filter in GATK4

I'm using GATK version4. After using VariantFiltration, I got the information of "PASS" of "not PASS". Next I want to filter out the "not PASS" variants. So I used the Selectvariants but, I can't filtered out the the not PASS variant well?
Please tell me how to use the -select argument.

Thank you

codes are as below
-----------------------------------
hkmac2017:exome_bam hirokikimura$ java -jar /Users/hirokikimura/exome_bam/gatk-4.1.2-2.0/gatk-package-4.1.2.0-local.jar SelectVariants -R human_g1k_v37_decoy.fasta -V combined_genotyped_filtered_snps_indels_mixed.vcf -select "FILTER == PASS" -O combined_genotyped_filtered_snps_indels_mixed.PASS.vcf
-------------------------------------

Best Answers

Answers

  • meganejinmeganejin Member
    Thanks to your suggestion, I can do that.
  • meganejinmeganejin Member
    Hi,
    I'm now analyzing bam files. I'm going to do the GATK Haplotypecalling.
    But, after samtool sort , picard remove duplicates, GATK recalibration, I find there are many QC-failed reads in bam file.
    Could you tell me I should remove the QC-failed reads in bam file before Haplotypecalling?

    meganejin
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @meganejin

    Take a look at our recommended best practices for data preprocessing: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11165

  • meganejinmeganejin Member
    Hi,
    Thank you for reply! It's very simple!
    Actually, I got multiple bam files after "Map to Refference" BWA from my collaborator.
    So, I performed MarkDuplicates by pocard and BaseRecalibrator by GATK4 for each bamfiles.
    The result is attached file.
    I asked you, because I saw many examples of bam files which don't have QC-failed reads.
    So, is it OK to perform the Haplotypecalling by GATK 4 despite the many QC-failed reads?
  • meganejinmeganejin Member
    Hi,

    Thank you very much for your detailed advice!!
    One more question, I want to analyze 700 bam files. So, I don't want to reduce the time of analyzing per sample.
    For each samples, so far I performed samtools-sort, Picard-FixmateInformation, Picard-Markduplication.
    However, in the GATK"best practice" you showed me last week, only MarkDuplicatesSpark is needed for the above three process.

    What I want to ask you is that if I perform GATK4-MarkDuplicatesSpark, I don't have to perform the samtools sort or Picard-FixmateInformation ?
    If so, I'm glad because many time will be saved.

    Best regards
  • meganejinmeganejin Member
    Hi,
    One more question,
    As your suggestion, I performed the MarkDuplicatesSpark from my bam file using below command.
    ----------------------------------
    java -jar /Users/hirokikimura/exome_bam/gatk-4.1.2-2.0/gatk-package-4.1.2.0-local.jar MarkDuplicatesSpark -I NC412.bam -O NC412.marked_duplicates.bam
    -------------------------------------
    But I can't look the "marked_duplicates.bam" file because of the fail to open the bam file.
    --------------------------------------------
    samtools flagstat NC412.marked_duplicates.bam
    [E::hts_hopen] Failed to open file NC412.marked_duplicates.bam
    [E::hts_open_format] Failed to open file NC412.marked_duplicates.bam
    ------------------------------------
    Furthermore, I can't perform the Basereacalibrator -GATK4 using the above NC412.marked_duplicates.bam because of the following commnet.
    -----------------------------------------
    java -jar /Users/hirokikimura/exome_bam/gatk-4.1.2-2.0/gatk-package-4.1.2.0-local.jar BaseRecalibrator -I NC412.marked_duplicates.bam -R human_g1k_v37_decoy.fasta --known-sites dbsnp_138.b37.vcf -known-sites Mills_and_1000G_gold_standard.indels.b37.vcf -O NC412_spark_recal.table

    A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.
    reference contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1, NC_007605, hs37d5]
    reads contigs = []
    ---------------------------------------------

    Are there any error for using MarkduplicatesSpark ?

    Best regards,
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    @meganejin

    1) MarkDuplicatesSpark processing can replace MarkDuplicates and SortSam steps but not Picard-FixmateInformation.

    2)

    I can't look the "marked_duplicates.bam" file because of the fail to open the bam file.

    Please validate you bam file using this tool https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_sam_ValidateSamFile.php

    3)

    A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.

    Can you please confirm that the the reference build that you used to align the reads match the reference build used in BaseRecalibrator?
    Please post the GATK versions and the exact commands you used for preprocessing.

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