Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bcftools call: why is this a 1/1?

    I can't for the life of me figure out why bcftools call genotypes this position (and many, many others like it) as 1/1:

    Here's the input VCF line:

    Code:
    10	227179	.	C	T,<*>	0	.	DP=191;I16=91,87,7,2,6502,238474,333,12321,235,3775,420,25200,3675,85899,97,1569;QS=0.733,0.267,0;VDB=0.00520152;SGB=-0.662043;RPB=0.000875247;MQB=0.0198712;MQSB=0.892843;BQB=0.980427;MQ0F=0.0209424	PL:DP:ADF:ADR:AD	64,255,0,255,27,95:187:91,7,0:87,2,0:178,9,0
    and here's the output from bcftools call -m :

    Code:
    10	227179	.	C	T	34.7149	.	DP=191;VDB=0.00520152;SGB=-0.662043;RPB=0.000875247;MQB=0.0198712;MQSB=0.892843;BQB=0.980427;MQ0F=0.0209424;AC=2;AN=2;DP4=91,87,7,2;MQ=3	GT:PL:DP:ADF:ADR:AD	1/1:64,255,0:187:91,7:87,2:178,9
    Note that DP4=91,87,7,2 -- there are 178 REF reads and 9 ALT reads used to make the call. How on earth is that ALT homozygous "1/1"??

    I hugely appreciate any explanation of this call!
    Sam Hokin
    Computational Scientist, Carnegie and NCGR

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM
  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 02:46 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-07-2024, 06:57 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-06-2024, 07:17 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-02-2024, 08:06 AM
0 responses
23 views
0 likes
Last Post seqadmin  
Working...
X