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liftOverVCF.pl error

blueskypyblueskypy Member ✭✭
edited February 2014 in Ask the GATK team

Could anyone help me with this error?

liftOverVCF.pl \
  -vcf NA12878.genotypes_chr1_CEU_r28_nr.b36_fwd.GenomeWideSNP_6.vcf \
  -chain $dbDir/b36tob37.chain \
  -out NA12878.genotypes_chr1_CEU_r28_nr.b37_fwd.GenomeWideSNP_6.vcf \
  -gatk GATK-2.8-1 \
  -newRef broad_bundle_b37_v2.8/human_g1k_v37.fasta \
  -oldRef iGenome/Homo_sapiens/NCBI/build36.3/Sequence/WholeGenomeFasta/genome.fa

The chain file is from https://github.com/broadgsa/gatk/tree/master/public/chainFiles

The error I got is this:
“##### ERROR MESSAGE: Bad input: the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference”

Thanks,

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    No idea why this is not working; try walking through the pl script progressively and see what it's stumbling on. Unfortunately we can't provide detailed support for this script, it's just provided as-is. Good luck!

  • blueskypyblueskypy Member ✭✭
    edited February 2014

    hi, Geraldine,
    Thanks for the help! I'll look into the code. I wonder if you happen to know how to get the common variants in NA12878? I guess I can

    1. find its whole genome SNP microarray data which should be common variants. But those are all based on b36

    2. or find a way to identify common variants in the GIB call set. but I don't know how to do that, any idea?

    Thanks,

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    What do you mean by common variants? You mean common in humans in general? Or to her ethnic cohort?

  • blueskypyblueskypy Member ✭✭

    Yes, common in humans in general.

  • blueskypyblueskypy Member ✭✭
    edited February 2014

    If I can just annotate the GIB call set with MAF info, then I can just select those with MAF>1% as common variant in human population. But how can I add the MAF info to the GIB call set? Seems VariantAnnotator does not do that.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    There is no MAF annotation available to VA; the way to do it is query the AFs using a JEXL expression. We've covered this previously in the forum (e.g. here. Note however that it's not currently possible to do this directly for multiallelic variants because of limitations of the JEXL system; it will only work for simple variants with only one ALT allele. That said you can also output the AFs to a table using VariantsToTable and analyze that in R (or whatever your favorite stats environment might be).

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