Hi sbstevenlee,
Thank you, I shall try this out.
• 0 views
•
link
written
by
ww22runner •
Duplicate results in vardict vcf
Hello everyone,
I am using Vardict to look for SNVs in an unpaired sample and this is the command I am using:
$VARDICT -G $REF_GENOME_b37 -f 0.03 -N "my_sample" -b "${SAMPLE_PFX}_UN.bam" -r 5 -z 1 -t -c 1 -S 2 -E 3 -g 4 $BEDFILE|sed '1d'|teststrandbias.R|var2vcf_valid.pl -N "unpaired" -f 0.03 -v 5 > ${SAMPLE_PFX}_vardict.vcf
However, whether I use the -t flag or -F 0x500 flag, I keep getting duplicate result rows in my vcf:
Both rows are the same and I cannot understand why the duplicate was not filtered, any advice would be greatly appreciated!
Thank you
• 2,184 views
•
link
updated
by
Ram
•
written
by
ww22runner •
•
written
by
ww22runner •
1 answer
If you are a Python user, you may want to check out the pyvcf submodule I wrote. If the duplicate rows are truly duplicate in the sense that all the fields are identical, you can clean up your VCF file this way:
>>> from fuc import pyvcf
>>> data = {
... 'CHROM': ['chr1', 'chr2', 'chr2'],
... 'POS': [100, 101, 101],
... 'ID': ['.', '.', '.'],
... 'REF': ['G', 'T', 'T'],
... 'ALT': ['A', 'C', 'C'],
... 'QUAL': ['.', '.', '.'],
... 'FILTER': ['.', '.', '.'],
... 'INFO': ['.', '.', '.'],
... 'FORMAT': ['GT', 'GT', 'GT'],
... 'Steven': ['0/1', '1/1', '1/1']
... }
>>> vf = pyvcf.VcfFrame.from_dict([], data)
>>> # vf = pyvcf.VcfFrame.from_file('your_file.vcf')
>>> vf.df
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Steven
0 chr1 100 . G A . . . GT 0/1
1 chr2 101 . T C . . . GT 1/1
2 chr2 101 . T C . . . GT 1/1
>>> df = vf.df.drop_duplicates()
>>> filtered_vf = pyvcf.VcfFrame([], df)
>>> filtered_vf.to_file('filtered.vcf')
>>> filtered_vf.df
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Steven
0 chr1 100 . G A . . . GT 0/1
1 chr2 101 . T C . . . GT 1/1
If your duplicate rows have the same POS, REF, ALT, ... but have slightly different genotype data for some reason, above will not work. Let me know if this is the case.
• 0 views
•
link
written
by
sbstevenlee •
Log in to answer this question.
More posts like this
-
VarDictJava - teststrandbias.R
written by accdg2022 •
-
variant calling error with VarDict
written by shubhamkumbhar420 •
-
How can I use PoN when running vardict?
written by oghzzang •
Do not open VCF files in Excel. Instead, get those two lines on the command line and use
uniqto find if they have the same content. If not, you have a lead to look for cause of difference. If they have the exact same content, an expert on VarDict would be in a better place to answer your question.Hello Ram, thank you for your suggestion, they are the same content. Somehow, using the
--deldupvaroption removes the duplicate but the-toption or-F 0x504, both of which should remove duplicates do not work. If you know the difference between these options, please do let me know, thanks.