Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Stand alone torrent variant caller -g request

    Hi!

    I am trying to run the stand alone torrent variant caller on an 18-month old BAM file that was aligned to some version of hg19

    I am at the point where the caller is objecting to the fact that there appear to be two different runs in the file (I think).

    Here is the error message:

    ERROR: Multiple Samples found in BAM file/s provided. Torrent Variant Caller currently supports variant calling on only one sample.
    ERROR: Please select sample name to process using -g parameter.

    I have absolutely no clue where to put the -g parameter as requested.

    I looked at the BAM files using the header commands in Bamtools and find that there appear to be two runs, one named: ID:Y2PAB and another called ID:ZKWV4

    Each looks like it was aligned against a slightly different (possibly) hg19. The first: LB:hg19 and the second: LB:hg19_ucsc

    When I try to figure out how to put in the -g using help on the python command, or just trying -g, I get:

    variant_caller_pipeline.py -g
    Usage: variant_caller_pipeline.py [options]

    variant_caller_pipeline.py: error: no such option: -g

    ergo, this appears to be a difficult problem…

    Suggestions? Work-arounds?

    I have found the Ion Torrent Sample Manager in GitHub that is giving rise to the error message, but
    I still have no solution to how to use -g

    Last edited by bgold04; 01-10-2015, 04:25 PM. Reason: tiny update

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM
  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:54 AM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-14-2024, 07:24 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-13-2024, 08:58 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-12-2024, 02:20 PM
0 responses
17 views
0 likes
Last Post seqadmin  
Working...
X