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samtools
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bcftools
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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Find unique SNP in a sample from a multisample VCF file
#2218
Sameerpython
opened
2 days ago
0
How does mpileup adjust-MQ actually work?
#2217
gmanthey
opened
2 days ago
0
bcftools norm shifts symbolic <DEL> to position 1 without warning if the END tag is missing from VCF
#2216
davmlaw
opened
2 days ago
0
bcftools 1.20 merge (--merge both) gvcfs results in more than one variant at the same location for very complex polyallelic MNP variants
#2215
jcm6t
opened
5 days ago
0
Bcftools view -i sMIN(FORMAT/DP)>=3 error
#2214
Evansd36
closed
1 week ago
2
Is there a way to filter on fraction of reads supporting an allele?
#2213
goeckeritz
opened
1 week ago
1
CSQ annotation - should be frameshift
#2212
JakeHagen
closed
5 days ago
4
BCFtools not calling variant, despite adequate coverage
#2211
mpiersonsmela
closed
2 weeks ago
3
GTcheck discrepancy between discordance score and the number of matching genotypes
#2210
leetde
closed
2 weeks ago
1
Merge error - duplicate sample names
#2209
desmodus1984
closed
1 week ago
1
Problem with plugin tests
#2208
pd3
opened
3 weeks ago
0
Speeding up bcftools merge for large number of vcf files with identical variant records containing sample genotypes.
#2207
rajwanir
closed
3 weeks ago
1
Possible isec memory leak
#2206
sandra-selfdecode
closed
1 week ago
1
[Solved] bcftools merge Failed to open *vcf.gz: could not load index
#2205
DLCrawford
closed
1 week ago
1
Ability to skip nonvariant records within a trio for mendelian2 plugin
#2204
ASLeonard
closed
3 weeks ago
1
Genotype Hard Calling- keeping GQ>=20, DP >=10 and 0.2<AB<0.8
#2203
sleibovitz
closed
1 week ago
5
bcftools annotate can output an INFO field with unquoted semicolons
#2202
jkmatila
closed
1 month ago
1
How to count number of haplotypes and haplotype frequency from phased vcf files?
#2201
Arline13
closed
1 month ago
1
bcftools concat --allow-overlaps produces output VCF with contigs out of order
#2200
TedBrookings
closed
1 month ago
5
norm remove dupes doesn't handle symbolic and non-symbolic duplicates
#2199
davmlaw
opened
1 month ago
2
Undefined header [W::vcf_parse] INFO 'PR' is not defined in the header, assuming Type=String
#2198
aainaGit
closed
1 month ago
1
Renaming .vcf.gz file using mv command and now bcftools won't recognise
#2197
kiran-lee
closed
1 month ago
1
How to compare several vcf files using bcftools
#2196
Arline13
closed
1 month ago
2
[merge] [view] Feature request: Ability to delete an unseen allele line if it duplicates an ALT-containing line
#2195
PlatonB
closed
1 month ago
4
Clarification on -e 0 flag and interpretation of discordance with PL-vs-PL and GT-vs-GT
#2194
goeckeritz
closed
1 month ago
3
Fix typos on the main develop branch
#2193
cmdcolin
closed
1 month ago
0
Fix typos on documentation in the gh-pages branch
#2192
cmdcolin
closed
1 month ago
1
consensus `>chr1:1-1` leads to error `FIXME: <chr>:<pos> .. idx=-<int>, ori_pos=<pos>`
#2191
Fan-iX
closed
1 month ago
1
Substring matching for variant IDs to aid in filtering records with multiple IDs?
#2190
rajwanir
closed
1 month ago
1
Apart from the header, bcftools mpileup did not output any other content
#2189
dongaoqian
closed
1 month ago
5
bcftools stats DP
#2188
fan040
closed
1 month ago
3
Parameter -q in bcftools does not work as specified
#2187
Lilu-guo
opened
1 month ago
1
Problem with binomial calculation
#2186
chundruv
opened
1 month ago
3
bcftools mpileup + call seemingly confident in allele only present in a few reads?
#2185
emos8710
opened
1 month ago
3
bcftools sort end indexs problem
#2184
DarioCannella
closed
1 month ago
0
Number of missing genotypes in bcftools stats
#2183
mufernando
closed
1 month ago
1
norm remove duplicates doesn't handle SVLEN, removes non-duplicate symbolic variants
#2182
davmlaw
closed
1 month ago
1
bcftools reference
#2181
felipeiani
closed
1 month ago
1
bcftools gtcheck --no-HWE-prob segfaults trying to access uninitialized args->nmatch array
#2180
freeseek
closed
1 month ago
1
Colons in VCF #CHROM columns are not parsed and throw error
#2179
groodri
closed
1 month ago
9
What is meant by 'but will not attempt to fix PL or other fields'?
#2178
swvanderlaan
closed
1 month ago
1
bcftools mpileup handling of corrupted/truncated data/streaming errors
#2177
kachulis
closed
1 month ago
3
Updating DP tag in the INFO field following subsetting (or merging) of samples
#2175
evcurran
closed
1 month ago
1
Work around ubuntu's latest clang compiler missing address sanitizer
#2174
jkbonfield
closed
1 month ago
0
"bcftools norm -m -any" prdocues "."
#2173
shahamer
opened
2 months ago
1
rs41303343 is defined as chr7:99652771 A -> AA duplication in GenBank and EnsEMBL
#2172
davidyuyuan
closed
2 months ago
8
new feature --force-single absent
#2171
pdimens
closed
2 months ago
1
bcftools view -S data size vcf
#2170
hitwbt
closed
1 month ago
1
Erroneous ROH output
#2169
snakesch
closed
2 months ago
1
Read depth and allele depth is low / zero
#2168
irbinveliz
closed
2 months ago
1
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