the reference allele mismatch and the annotation program give me Invalid alternative alleles

AbdelazizAbdelaziz Member
edited January 4 in Ask the GATK team
Lifting variants over and sorting (not yet writing the output file.)
INFO 2019-01-02 21:12:31 LiftoverVcf Processed 116415 variants.
INFO 2019-01-02 21:12:31 LiftoverVcf 0 variants failed to liftover.
INFO 2019-01-02 21:12:31 LiftoverVcf 31704 variants lifted over but had mismatching reference alleles after lift over.
INFO 2019-01-02 21:12:31 LiftoverVcf 27.2336% of variants were not successfully lifted over and written to the output.
INFO 2019-01-02 21:12:31 LiftoverVcf liftover success by source contig:
INFO 2019-01-02 21:12:31 LiftoverVcf 1: 84711 / 116415 (72.7664%)
INFO 2019-01-02 21:12:31 LiftoverVcf lifted variants by target contig:
INFO 2019-01-02 21:12:31 LiftoverVcf 1: 84711
WARNING 2019-01-02 21:12:31 LiftoverVcf 29374 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO 2019-01-02 21:12:31 LiftoverVcf Writing out sorted records to final VCF.
[Wed Jan 02 21:12:50 CST 2019] picard.vcf.LiftoverVcf done. Elapsed time: 1.09 minutes.


  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    @Abdelaziz - Could you please provide the command that was run? Also, what version of GATK are you using? Also, please tell us where you got your chain file from? We recommend those from UCSC.

  • AbdelazizAbdelaziz Member
    edited January 5
    first, Thank you so much for your fast reply

    I used version: picard-2.18.21

    that is my command

    java -jar picard.jar LiftoverVcf \
    I=test_1_vcf.vcf \
    O=lifted_over_b37.vcf \
    CHAIN=b36tob37.chain \
    REJECT=rejected_variants_b37.vcf \
    R=human_g1k_v37.fasta \

    the chain file I used from your website

    I make the imputation process using the reference (hapmap3)

    that is the part of test_1_vcf.vcf

    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 014_S_0520 005_S_1341 012_S_1175 012_S_0803 018_S_0055 027_S_0118 027_S_0403 053_S_0389 041_S_0262 005_S_1224 010_S_0472 098_S_0171 099_S_0470 128_S_0245 137_S_0825 128_S_0266 067_S_0243 016_S_1138 033_S_1116 007_S_0070 133_S_1170 128_S_0522 141_S_1245 .....
    1 742584 rs3131972 G A . . PR GT 0/0 0/0 0/1 0/0 .......
    Post edited by Abdelaziz on
  • AbdelazizAbdelaziz Member
    can you help me
  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    @Abdelaziz I am working on this for you this morning. The forum is not tended on the weekends or at night.

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    @Abdelaziz One potential issue is that you may not be running the latest version of Picard tools, which may or may not be causing this issue. Here is the latest version. Could you please try that out?

  • AbdelazizAbdelaziz Member
    Thank you so much for helping me, I will use the latest version
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