Question: Lowercase variants reported by SomaticSniper
0
gravatar for Inés Sentís
16 months ago by
Inés Sentís10 wrote:

Hi!

First of all, sorry if this is a very naive question but I could not find the answer in the user's manual of SomaticSniper . Question: why there are some reported variants in the VCF output of SomaticSniper in lowercase? What does that mean?

#CHROM  POS     ID  REF     ALT     QUAL    FILTER  INFO    ...
    1   575876  .   G   C   .   .   .   
    1   821143  .   g   T   .   .   .   
    1   825104  .   g   A   .   .   .
ADD COMMENTlink modified 16 months ago by Pierre Lindenbaum114k • written 16 months ago by Inés Sentís10
1
gravatar for Pierre Lindenbaum
16 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum114k wrote:

these are the lower-case bases in your REFerence.

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr1.fa.gz" | gunzip -c | grep -v ">" |  grep -o '.'   | nl | grep -w -E '(575876|821143|825104)'
575876  G
821143  g
825104  g

in the UCSC, the lower-cases bases overlap a region with a repeat ( http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ )

  • chr*.fa.gz: compressed FASTA sequence of each chromosome.

Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case.

ADD COMMENTlink modified 16 months ago • written 16 months ago by Pierre Lindenbaum114k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 937 users visited in the last hour