Lowercase variants reported by SomaticSniper

Question

[Inés Sentís]

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   .   .   .

Answer 1

[Pierre Lindenbaum]

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.