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Can Picard LiftoverVcf handle Indels?

Dear GATK team,

I have successfully run Picard LiftoverVcf on SNPs only data but when Combined with Indels, the results file is empty.
I use Picard version: 2.18.16. I now wonder if Picard LiftoverVcf is able to handle SNPs. If not, which tool would you recommend? For instance, would LiftOverIntervalList work for Indels?

Thank you

Best Answers

  • modi2020modi2020
    Accepted Answer

    Thank you so much Bhanu.
    Yep. It turns out that the file where the SNPs and Indels are combined needed some amendments. I had to remove and/or rename entire chromosomes in it. LiftoverVcf now works on it fine.
    Thank you so much for your help with this.

    Have a great day!

Answers

  • modi2020modi2020 Member

    Sure.
    I ran the following command for remapping the SNPs alone:
    java -Xms10G -Xmx15G -jar picard.jar LiftoverVcf \
    I=6.horses.filtered.snps.vcf \
    O=lifted_over.vcf \
    CHAIN=equCab2ToEquCab3.over.chain \
    REJECT=rejected_variants.vcf \
    RECOVER_SWAPPED_REF_ALT=true \
    R=/ufrc/brooks/malabri/6Horse/EquCab3.0_UCSC/equCab3.fa

    There was an output in the file "lifted_over.vcf" without problems.

    The command on the file that has both SNPs and Indels was as follows:
    java -Xms10G -Xmx15G -jar picard.jar LiftoverVcf \
    I=SNPs_Indels_combined.vcf \
    O=lifted_over1.vcf \
    CHAIN=equCab2ToEquCab3.over.chain \
    REJECT=rejected_variants1.vcf \
    RECOVER_SWAPPED_REF_ALT=true \
    R=/ufrc/brooks/malabri/6Horse/EquCab3.0_UCSC/equCab3.fa

    However, this time, the output file was empty.

    So, I am wondering if its the Indels that cause the matter?
    If so, would LiftOverIntervalList work?

    Thank you so much

  • modi2020modi2020 Member
    Accepted Answer

    Thank you so much Bhanu.
    Yep. It turns out that the file where the SNPs and Indels are combined needed some amendments. I had to remove and/or rename entire chromosomes in it. LiftoverVcf now works on it fine.
    Thank you so much for your help with this.

    Have a great day!

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