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SortVcf on mm10 vcf does not seem to be reordering contigs successfully in same order as mm10.dict

ekofmanekofman Member, Broadie

Hi,

I'm trying to reorder a VCF's contigs to match my mm10.fa contigs

I run java -jar $PICARD_PATH SortVcf I=mouseGCT_family_merged.filtered.copy.vcf O=mouseGCT_family_merged.filtered.sorted.vcf SEQUENCE_DICTIONARY=mm10.dict

This mm10.dict was generated just now from my mm10.fa.

However, then when I try running VariantsToTable I get this error:

##### ERROR MESSAGE: Input files variant and reference have incompatible contigs. Please see https://software.broadinstitute.org/gatk/documentation/article?id=63for more information. Error details: The contig order in variant and reference is not the same; to fix this please see: (https://www.broadinstitute.org/gatk/guide/article?id=1328),  which describes reordering contigs in BAM and VCF files..
##### ERROR   variant contigs = [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr1_GL456210_random, chr1_GL456211_random, chr1_GL456212_random, chr1_GL456213_random, chr1_GL456221_random, chr2, chr3, chr4, chr4_GL456216_random, chr4_GL456350_random, chr4_JH584292_random, chr4_JH584293_random, chr4_JH584294_random, chr4_JH584295_random, chr5, chr5_GL456354_random, chr5_JH584296_random, chr5_JH584297_random, chr5_JH584298_random, chr5_JH584299_random, chr6, chr7, chr7_GL456219_random, chr8, chr9, chrM, chrUn_GL456239, chrUn_GL456359, chrUn_GL456360, chrUn_GL456366, chrUn_GL456367, chrUn_GL456368, chrUn_GL456370, chrUn_GL456372, chrUn_GL456378, chrUn_GL456379, chrUn_GL456381, chrUn_GL456382, chrUn_GL456383, chrUn_GL456385, chrUn_GL456387, chrUn_GL456389, chrUn_GL456390, chrUn_GL456392, chrUn_GL456393, chrUn_GL456394, chrUn_GL456396, chrUn_JH584304, chrX, chrX_GL456233_random, chrY, chrY_JH584300_random, chrY_JH584301_random, chrY_JH584302_random, chrY_JH584303_random]
##### ERROR   reference contigs = [chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr1_GL456210_random, chr1_GL456211_random, chr1_GL456212_random, chr1_GL456213_random, chr1_GL456221_random, chr2, chr3, chr4, chr4_GL456216_random, chr4_JH584292_random, chr4_GL456350_random, chr4_JH584293_random, chr4_JH584294_random, chr4_JH584295_random, chr5, chr5_JH584296_random, chr5_JH584297_random, chr5_JH584298_random, chr5_GL456354_random, chr5_JH584299_random, chr6, chr7, chr7_GL456219_random, chr8, chr9, chrM, chrX, chrX_GL456233_random, chrY, chrY_JH584300_random, chrY_JH584301_random, chrY_JH584302_random, chrY_JH584303_random, chrUn_GL456239, chrUn_GL456367, chrUn_GL456378, chrUn_GL456381, chrUn_GL456382, chrUn_GL456383, chrUn_GL456385, chrUn_GL456390, chrUn_GL456392, chrUn_GL456393, chrUn_GL456394, chrUn_GL456359, chrUn_GL456360, chrUn_GL456396, chrUn_GL456372, chrUn_GL456387, chrUn_GL456389, chrUn_GL456370, chrUn_GL456379, chrUn_GL456366, chrUn_GL456368, chrUn_JH584304]
##### ERROR ------------------------------------------------------------------------------------------

Why aren't the contigs getting sorted correctly? For example you can see that the order of chr4_GL456350_random and chr4_JH584292_random is reversed in the sorted vcf compared to the fasta dict.

Based on other forum postings, guessing @Sheila might be best poised to help out with this. Thanks in advance!

Answers

  • ekofmanekofman Member, Broadie

    Hmm seems like the tool might be auto-generating an index file for the unsorted contigs instead of the sorted contigs...

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hi @ekofman - Were the articles in the error message any help?

    Also, it seems that Picard Tools syntax has been updated. I am not sure if this will resolve the error, but you might want to try the command with the new syntax.


    ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) **********
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