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Fasta Alternate Reference Maker Ignoring Insertions

Gretna20Gretna20 Madison, WIMember

I seem to be having an issue with the Fasta Alternate Reference Maker. Within my bam file and well as the vcf file there are notated insertions in 100% of the reads. When a fasta is created this insertion seems to be ignored. All of the noted deletions and mutations are carried over into the fasta file but insertions (1-3bp) seem to be ignored. I am looking at the bam files and vcf files on IGV so can see where individual mutations are.

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @Gretna20
    Hi,

    Can you please post the exact command you ran and the version of GATK you are using? Please also post an example record from the VCF with an insertion and the corresponding output in the FASTA file.

    Thanks,
    Sheila

  • PRASADLIFEPRASADLIFE LucknowMember

    Hi,
    I face the same problem where fasta alternate reference maker, ignoring the indels. I need an alternate fasta files where both SNPs and indels are incorporated.

    This is my command:-
    java -jar /home/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R /home/all_arab.fa -o sample_vcf.txt -V sample.vcf -L 1:1-150

    This is my sample.vcf file:-

    fileformat=VCFv4.1

    FILTER=<ID=q25,Description="Quality below 25">

    INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">

    FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

    FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">

    FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">

    FILTER=<ID=q30,Description="Quality below 30">

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 10011

    1 51 . A TA 32 PASS DP=11 GT:GQ:DP 0|0:32:11
    1 52 . T . 32 PASS DP=11 GT:GQ:DP 0|0:32:11
    1 53 . C . 32 PASS DP=11 GT:GQ:DP 0|0:32:11
    1 55 . C . 32 PASS DP=11 GT:GQ:DP 0|0:32:11
    1 56 . T . 32 PASS DP=11 GT:GQ:DP 0|0:32:11
    1 58 . A . 32 PASS DP=10 GT:GQ:DP 0|0:32:10
    1 59 . A GC 32 PASS DP=11 GT:GQ:DP 0|0:32:11
    1 60 . T . 32 PASS DP=10 GT:GQ:DP 0|0:32:10
    1 61 . C . 32 PASS DP=8 GT:GQ:DP 0|0:32:8
    1 64 . T . 30 PASS DP=7 GT:GQ:DP 0|0:30:7
    1 127 . T . 32 PASS DP=3 GT:GQ:DP 0|0:32:3
    1 128 . T . 32 PASS DP=3 GT:GQ:DP 0|0:32:3
    1 129 . G . 32 PASS DP=3 GT:GQ:DP 0|0:32:3
    1 130 . A . 27 PASS DP=2 GT:GQ:DP 0|0:27:2
    1 131 . A . 27 PASS DP=2 GT:GQ:DP 0|0:27:2
    1 132 . A . 32 PASS DP=3 GT:GQ:DP 0|0:32:3
    1 133 . A G 27 PASS DP=2 GT:GQ:DP 0|0:27:2
    1 134 . T . 32 PASS DP=3 GT:GQ:DP 0|0:32:3
    1 136 . A . 34 PASS DP=3 GT:GQ:DP 0|0:34:3
    1 137 . T . 34 PASS DP=3 GT:GQ:DP 0|0:34:3
    1 138 . T . 34 PASS DP=3 GT:GQ:DP 0|0:34:3
    1 139 . G . 34 PASS DP=3 GT:GQ:DP 0|0:34:3
    1 140 . T . 34 PASS DP=4 GT:GQ:DP 0|0:34:4
    1 141 . G . 34 PASS DP=4 GT:GQ:DP 0|0:34:4
    1 142 . T . 36 PASS DP=4 GT:GQ:DP 0|0:36:4
    1 143 . A . 36 PASS DP=4 GT:GQ:DP 0|0:36:4
    1 144 . T . 36 PASS DP=4 GT:GQ:DP 0|0:36:4
    1 145 . A . 36 PASS DP=4 GT:GQ:DP 0|0:36:4
    1 146 . T ACG 36 PASS DP=4 GT:GQ:DP 0|0:36:4
    1 147 . A . 38 PASS DP=4 GT:GQ:DP 0|0:38:4
    1 148 . A . 38 PASS DP=4 GT:GQ:DP 0|0:38:4
    1 149 . T . 38 PASS DP=4 GT:GQ:DP 0|0:38:4
    1 150 . G . 38 PASS DP=4 GT:GQ:DP 0|0:38:4
    1 151 . A . 38 PASS DP=4 GT:GQ:DP 0|0:38:4
    1 152 . T . 38 PASS DP=4 GT:GQ:DP 0|0:38:4
    1 153 . A TC 38 PASS DP=4 GT:GQ:DP 0|0:38:4

  • SheilaSheila Broad InstituteMember, Broadie admin

    @PRASADLIFE
    Hi,

    Can you post an example VCF record and output reference where the indel is being ignored? The sites you posted all look like they have hom-ref genotypes assigned.

    -Sheila

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