How does variant callers deal with N in the reference sequence?
If there is an N in the reference genome, after the variant calling pipeline, if an alternative base (A/T/G/C) is called at the same position, will it be output in the VCF? Or any variants with the N in the reference will be ignored? Thanks!
• 1,438 views
•
link
updated
by
Ram
•
written
by
pyjiang2 •
•
written
by
pyjiang2 •
1 answer
Log in to answer this question.
More posts like this
-
Generating Positional List from VCF
written by Ared445 •
-
Extracting Read and mates having variant positions Using BAM file vcf file in Python using pysam/ b…
written by Hassan •
-
Is there a way to force a specific order for variants in a PLINK file that have the same chromosome…
written by curious
-
How to add sequence information to vcf from MPileup
written by helge.fluess •
-
NCBI Genome Remapping Service- clinical remap result difference with UCSC hg19
written by Sudhir Jadhao
-
Combining vcf files so that same loci data is combined
written by spiral01
-
Is there a base that will be ignored in variant calling
written by L. A. Liggett
-
Variant effect prediction on non-vcf format file
written by GR
-
Does VarScan default to reference base when thresholds not met?
written by fixtgear •
-
Why Does Vcf Aggregate Indels Like This?
written by Jeremy Leipzig
