Skip to content
Permalink
Browse files

improve markdown portions

  • Loading branch information...
lmoncla committed Jun 11, 2019
1 parent 75d12a5 commit 269b994874e65da8689561c27dec7e8429ed108b
Showing with 1 addition and 4 deletions.
  1. +1 −4 scripts/VCF annotater.ipynb
@@ -8,10 +8,7 @@
"\n",
"May 1, 2018 \n",
"\n",
"I found yet another issue with SNPEff this week. It seems that it has difficulty parsing through M2 sequences and combining the 2 coding regions together and treating them as a single coding region. I had one sample that was parsed correctly, but from my discussions with Pablo, it seems like for that to be the case you need to provide SNPEff with the gene sequences, gtf, and the translated protein sequences. That is too much work for each individual genome, and so I have decided that I am just going to write my own for now. There are a few caveats to this that are important to note: \n",
"\n",
"1. As of now, this will only output SNPs that fall within coding regions, which is probably a thing that I should fix later on. \n",
"2. As of now, it cannot handle anything more than 2 coding regions being combined into 1. This feature could absolutely be added, but I just did not do it yet. "
"I was having trouble with SNPEff mis-annotating coding region changes in M2 and NEP, so I decided to write my own. This is a simple notebook that will read in the reference sequences that reads were mapped to, a gtf file for those references sequences with coding region coordinates, and a vcf file output by Varscan. It will then determine whether SNVs occur within a coding region, and if so, annotate as amino acid changing or not. Currently, this will not annotate SNVs that fall outside of a coding region. "
]
},
{

0 comments on commit 269b994

Please sign in to comment.
You can’t perform that action at this time.