Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • CrossMap analysis

    I am trying to convert some genome coordinates of SNPs in one vcf file using the CrossMap program (http://crossmap.sourceforge.net/).

    I am having difficulties with the conversion. My vcf file does not have all chromosomes present in the chain file (for example chromosome random, etc), so the conversion is not performed.

    Do I need to remove all chromosomes not present in my vcf file from the chain file? (and maybe from the fasta file as well?)

    My error message was:
    KeyError: "sequence 'chr10_NT_461738v1_random' not present"

    This sequence is present only in the chain file, but I am not sure if I should edit the chain file.

    Also, Is the chromosome format need to be the same in the 3 files (input, chain and fasta file): Chr1, chr1 or 1?

    thanks

  • #2
    Originally posted by clarissaboschi View Post
    I am trying to convert some genome coordinates of SNPs in one vcf file using the CrossMap program (http://crossmap.sourceforge.net/).

    I am having difficulties with the conversion. My vcf file does not have all chromosomes present in the chain file (for example chromosome random, etc), so the conversion is not performed.

    Do I need to remove all chromosomes not present in my vcf file from the chain file? (and maybe from the fasta file as well?)

    My error message was:
    KeyError: "sequence 'chr10_NT_461738v1_random' not present"

    This sequence is present only in the chain file, but I am not sure if I should edit the chain file.

    Also, Is the chromosome format need to be the same in the 3 files (input, chain and fasta file): Chr1, chr1 or 1?

    thanks
    The error message "sequence 'chr10_NT_461738v1_random' not present" was not issued by CrossMap itself, it could be issued by its dependent package like pysam.

    My guess is "chr10_NT_461738v1_random" presents in your VCF file, but absent from your reference FASTA file.

    Comment


    • #3
      Ok, thanks I will check it. I tried by using bed file format and it worked very well.

      Comment


      • #4
        Originally posted by clarissaboschi View Post
        Ok, thanks I will check it. I tried by using bed file format and it worked very well.
        It further confirms my hypothesis. Pysam tried to retrieve the reference allele from FASTA file, it reported this error message when it failed to find
        'chr10_NT_461738v1_random'.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        50 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X