Hello,
After I run the samtools variant calling pipeline, I'm not getting the conventional .vcf output that I was expecting. Any advice or insight would be greatly appreciated.
Here is my command:
$ samtools mpileup -gf /scratch/$USER/Trinity.adj.fasta NFS_6525_adj_bowtie2.coordSorted.bam NFS_50254_adj_bowtie2.coordSorted.bam SFS_CC1_adj_bowtie2.coordSorted.bam SFS_25428_adj_bowtie2.coordSorted.bam | bcftools view -bvcg - > NFS_6525_50254_SFS_CC1_25428_adj_var.bcf
$ bcftools view NFS_6525_50254_SFS_CC1_25428_adj_var.bcf | vcfutils.pl varFilter -D 100 - > NFS_6525_50254_SFS_CC1_25428_adj_var.flt.vcf
I used VIM to view my NFS_6525_50254_SFS_CC1_25428_adj_var.flt.vcf file and it does not look like any examples that I've seen online. It's a combination of alpha-numeric characters and a list of my Trinity contigs. I've copied a sample of my .vcf file below:
(there is a full list of my Trinity contigs, a list of ~700 thousand),
contigID=TRINITY_DN311005_c0_g1_i1,length=296,IDX=667121>
and then a massive list of alpha-numeric characters which I cannot make sense of.
(some of the alphanumeric characters were changed to symbols when I copied and pasted here) T7<> õ @ ¸B P–E °B rE HB @œD % @ 1 , { . H G7<> õ @ ÚB èÓE °B rE HB @œD % @ 1 , "{ . I G7<> õ @ äB áE °B rE HB @œD % @ 1 , &{ . J G7<> õ @ äB áE °B rE HB @œD % @ 1 , &{ . K G7<> õ @ äB áE °B rE HB @œD % @ 1 , &{ . L G7<> õ @ äB áE °B rE HB @œD % @ 1 , &{ . M G7<> õ @ äB áE °B rE HB @œD % @ 1 , &{ . N A7<> õ @ àB ÝE °B rE HB @œD % @ 1 , ${ . O G7<> õ @ ÞB ÈÚE °B rE HB @œD % @ 1 , #{ . P T7<> õ @ ÀB šE °B rE HB @œD % @ 1 , #{ . Q C7<> õ @ ÜB ÏE °B rE HB @œD % @ 1 , &{ . R T7<> õ @ àB @ØE °B rE HB @œD % @ 1 , &{ . S A7<*> õ @ äB áE °B rE HB
However, my output looks nothing like the .vcf outputs that I found online.
Thank you.
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Hello michbrown!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=208748#post208748
This is typically not recommended as it runs the risk of annoying people in both communities.
what is the output of
and
So, it turns out I was running discordant versions of bcftools and samtools. I knew that they needed to be the same version, but the version that automatically loads into my environment was being used instead of the one in my directory. Thanks for getting back to me, I really appreciate that.
Cheers!