Question: Freebayes Variant calling
gravatar for manojkumarbioinfo
4.2 years ago by
manojkumarbioinfo60 wrote:

Hi, All I'm New to NGS analysis, i want to compare a variant's from different aligner (BWA,Bowtie,Novoalign) Freebayes variant calling program. while doing for Indel i found the command in in freebayes which used for Ignoring SNP alleles.

The command and the argument i have used in given below

./Tools/freebayes/bin/freebayes -f Reference/Reference/human_g1k_v37.fasta -I -X -u -v Output/Novoalign/Variant/Novoalign_InDel_freebayes.vcf Output/Novoalign/Alignment/Novoalign_realignment_recal.bam

Now if i run this my program runs but it stops at certain position saying the following message.

variant at 1:32170247


alt is empty

and i'm getting the vcf file of 1 mb till the exact position in chromosome 1

If i run the arguments which Ignore insertion and deletion alleles. I'm getting an file size of 1gb with all the chromosome.

I dont know why it stuck at particular postion the same follows for different aligner such as BWA or Novoalign or bowtie it stuck at certain position and ends the program

Does any one knows why ?

freebayes ngs • 2.7k views
ADD COMMENTlink modified 4.2 years ago by bedeabc110 • written 4.2 years ago by manojkumarbioinfo60
gravatar for bedeabc
4.2 years ago by
United Kingdom
bedeabc110 wrote:

I'd consider cross posting to the Google Group!forum/freebayes

ADD COMMENTlink written 4.2 years ago by bedeabc110
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