Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Invalid VCF files from Lifescope - allele "-"

    I found some problematic VCF files created by Lifescope software. The sequencing was done on Solid 5500. These VCFs cannot be merged with other VCF files. The variants in these files are all indels. When I run vcf-validator it seems the "-" in the allele is the problem. Some vcf-validator output:

    [lifescope@scyld small.indel]$ perl -I/home/lifescope/bin/vcftools_0.1.11/perl /home/lifescope/bin/vcftools_0.1.11/bin/vcf-validator 37_1_3/2013_08_13_exome_high.gff3.vcf
    Warning: The file is not sorted, for example chr12:53690189 comes after chr12:53690191
    chr12:53690189 .. Could not parse the allele(s) [-]
    [lifescope@scyld small.indel]$ perl -I/home/lifescope/bin/vcftools_0.1.11/perl /home/lifescope/bin/vcftools_0.1.11/bin/vcf-validator 37_1_4/2013_08_13_exome_high.gff3.vcf
    Warning: The file is not sorted, for example chr11:108100105 comes after chr11:108100112
    chr11:108100105 .. Expected combination of A,C,G,T,N for REF, got [-], the offending chars were [-]

    Does any other Lifescope user have the same problem? Is there an easy way to fix this? Thank you in advance!

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
19 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
22 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Working...
X