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

deletion:7:

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 ?