Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • picardtools LiftoverVcf losing majority of information

    I'm currently attempting to lift over variants from a .vcf file mapped to the hg18 assembly to the chimpanzee panTro4 assembly (UCSC nomenclature used here). I'm using the picardtools LiftoverVcf to accomplish this, as well as the .chain file available on UCSC.

    I'm noticing that only about 10% of variants are being lifted over, the rest are ending up in the 'regected' variants file. I'm wondering if this should be expected when lifting over from one organism to another, or if this is a strange occurrence.

    Note: the original .vcf (which used hg18 assembly as the reference) was produced with short reads from chimpanzees. So, my guess (if it this is not a bug in the picardtools program) is that the vast majority of "variants" picked up in the .vcf are, in fact, just fixed differences between human and chimpanzee.

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, 06-07-2024, 06:58 AM
0 responses
179 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-06-2024, 08:18 AM
0 responses
228 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-06-2024, 08:04 AM
0 responses
184 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-03-2024, 06:55 AM
0 responses
18 views
0 likes
Last Post seqadmin  
Working...
X