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chasewnelson / SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
GNU General Public License v3.0
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Problem with VCF #5

Closed DRL closed 8 years ago

DRL commented 8 years ago

Hi,

I was trying to use your software with a SNPeff annotated VCF file that I built using freebayes from several (pooled) samples ...

I am aware this is probably not the default format your software is expecting, but I was wondering whether you could give me a hint as to how I should modify the VCF to make it work.

I attached a sample.vcf.txt

The error(s) I got are below:

cheers,

dom 

>> snpgenie-1.2.pl --sepfiles --minfreq=0.01 --snpreport=Gr_pops.vs.nGr.v1.1.GQ.vcf.norm.filtered.final.snpeff.vcf --fastafile=nGr.v1.1.fa --gtffile=nGr.v1.1.augustus.manual.2015_03_23.gtf 

################################################################################
##                                                                            ##
##                             SNPGenie Initiated!                            ##
##                                                                            ##
################################################################################

  ###############################  LICENSE:  #################################
  ##              SNPGenie Copyright (C) 2015 Chase W. Nelson               ##
  ##            This program comes with ABSOLUTELY NO WARRANTY;             ##
  ##     This is free software, and you are welcome to redistribute it      ##
  ##               under certain conditions; see LICENSE.txt.               ##
  ############################################################################

There is 1 FASTA file in the working directory. ONE-SEQUENCE MODE activated...

Your MIN. MINOR ALLELE FREQ. is 0.01. All variants falling below this frequency will be ignored...

###########################  CURRENTLY PROCESSING:   ###########################
../../final/Gr_pops.vs.nGr.v1.1.GQ.vcf.norm.filtered.final.snpeff.vcf... VCF format detected

Converting ../../final/Gr_pops.vs.nGr.v1.1.GQ.vcf.norm.filtered.final.snpeff.vcf to SNPGenie format... 

In file ../../final/Gr_pops.vs.nGr.v1.1.GQ.vcf.norm.filtered.final.snpeff.vcf, the newline type is: Unix (LF, \n)

### FILE TYPE NOT FULLY SUPPORTED###

### FILE TYPE NOT FULLY SUPPORTED###

### FILE TYPE NOT FULLY SUPPORTED###

### FILE TYPE NOT FULLY SUPPORTED###

### FILE TYPE NOT FULLY SUPPORTED###

### FILE TYPE NOT FULLY SUPPORTED###
singing-scientist commented 8 years ago

I'm sorry that I did not realize an issue had been opened. The VCF you have attached does not seem to fit any of the standard specifications, probably because we have not used freebayes output before. Will get to this shortly; thanks for your patience...

singing-scientist commented 8 years ago

It would be helpful if you could email one full example VCF along with the GTF and FASTA, so I can make sure all issues peculiar to this particular VCF output style are supported. Would you be willing to do this? nelsoncw AT email DOT sc DOT edu

singing-scientist commented 8 years ago

Please re-open an issue if this has not been resolved.