Attention:
The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

Geraldine_VdAuwera admin

Folks, I'm sorry but I can't respond to questions on this page. Please post your questions in the public forum.

About

Username
Geraldine_VdAuwera
Location
Cambridge, MA
Joined
Visits
6,044
Last Active
Roles
Member, Administrator, Broadie
Points
8,127
Badges
34

Activity

  • Jourjina
    Hi Geraldine,
    I've been having some trouble getting gatk to work for me. the error i am stuck at currently is at the MarkIlluminaAdapters and the error I get is Two reads with same name but not correctly marked as 1st/2nd of pair: 700593F:583:HTWJMBCXX:1:1101:0:0

    can you please help me? my email address is
    [email protected]
    April 3
  • XiaoshenYin

    Hello @Geraldine_VdAuwera,

    As you responded in an earlier message:

    "Potentially, yes. If you have different expression of two alleles, and one is very low, you may not be able to call them correctly -- e.g. you may call the wrong genotype, or miss the call altogether (if it looks hom-ref).

    I am calling variants with RNAseq data using gatk. Since the missing call for hom-ref (i.e. 0/0) may affect the calculation of heterozygosity of a population a lot, is it possible to recover 0/0? If not, how should I properly deal with loci with 0/0 so that the heterozygosity will not be biased?

    In my vcf files from gatk, missing genotypes are represented in two ways, "./." and ".". Although documentations indicate that they represent diploid and haploid genotypes that are missing, it is still unclear why they are different. Could you please provide some hints on what may generate "./." and "."? Also, is "." actually hom-ref (i.e. 0/0)?

    Thanks.

    February 18