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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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Can we use bcftools to create genome based on cram file
#2300
HelloWorldLTY
opened
1 day ago
0
Filtering out indels but keeping invariant sites
#2299
ja-Reeve
opened
1 day ago
0
Add support for matching VCF lines by ID
#2298
pd3
opened
2 days ago
0
Issue with bcftools annotate
#2297
HVHunt
opened
4 days ago
0
Make --write-index work with concat with vcf (version 2)
#2296
whitwham
closed
1 day ago
0
Warning: fewer CSQ fields than expected
#2295
kuaileshizuihao
opened
6 days ago
0
bcftools csq: Change chromosome name requirement.
#2294
niederhuth
opened
6 days ago
0
Error "Failed to read from standard input: unknown file type" with Gzipped BAM Files
#2293
Silvia-lme
opened
1 week ago
0
Sampling frequency field not found in the header. Please check the header fields.
#2292
wahibalkamat2
opened
1 week ago
0
BCFtools norm dropping duplicates options: is -d none equivalent to -d exact and -D ?
#2291
davidjakubosky
opened
1 week ago
0
Is BCFtools norm guaranteed to maintain sort order?
#2290
davidjakubosky
closed
1 day ago
1
CI improvements
#2289
jkbonfield
opened
1 week ago
0
Fix cut and paste errors in writing the get_data.sh script.
#2288
jkbonfield
closed
1 day ago
1
How to populate Fisher test annotation
#2287
pd3
opened
1 week ago
1
bcftools concat segfault if VCF files contain only headers
#2286
dpryan79
opened
1 week ago
3
Bcftools merge
#2285
desmodus1984
closed
1 week ago
1
`--output-type u --write-index=tbi` writes csi index
#2284
fellen31
closed
1 week ago
1
Make --write-index work for concat with vcf (needs htslib#1839)
#2283
whitwham
closed
4 days ago
1
Make the mpileup BAM_CREF_SKIP filter optional.
#2282
jkbonfield
opened
2 weeks ago
0
Remove the mpileup BAM_CREF_SKIP filter.
#2281
jkbonfield
opened
2 weeks ago
2
Document / Improve / Polish / Fix --indels-2.0
#2280
jkbonfield
opened
2 weeks ago
3
split-vep AF
#2279
andrew2k
closed
1 week ago
1
Bcftools view error about an invalid tag "1000gALT", how do I fix this?
#2278
PVlasov93
closed
1 week ago
1
Significant difference between IDV and AD when calling certain RNA-seq indels with mpileup
#2277
luyh-xp
opened
3 weeks ago
8
Variable expansion issue with +setGT? [$VARIABLE-] isn't working...
#2276
goeckeritz
opened
3 weeks ago
1
Work around an incompatibility between Perl and clang warnings.
#2275
jkbonfield
closed
3 weeks ago
1
Reapply previous Makefile dependency fix
#2274
jmarshall
closed
3 weeks ago
0
annotate add INFO/tag form CHROM-POS-REF-ALT
#2273
user-tq
opened
4 weeks ago
0
Miscellaneous minor header and dependency fixes
#2272
jmarshall
closed
4 weeks ago
1
Extract a list of mean values from format tags (e.g., DP, GC, IGC, etc.) per position
#2271
andreasgoteson
closed
2 days ago
4
How to correct VCF header with extra space/tab in it
#2270
desmodus1984
closed
3 weeks ago
1
Pipe into bcftools view with region specification
#2269
gevro
closed
1 month ago
2
Permanent configuration of BCFTOOLS_PLUGINS path
#2268
gevro
closed
1 month ago
5
BCFtools "--write-index=tbi" and `bcftools index --tbi` generate different index files
#2267
freeseek
closed
3 weeks ago
3
bcftools merge produces segmentation fault
#2266
vidprijatelj
closed
3 weeks ago
1
Fix a regression with -Ou format being the same as -Ob.
#2265
jkbonfield
closed
4 weeks ago
1
annotate ID for multi-allelic sites
#2264
ikarus97
opened
1 month ago
1
Incorrect compression on `view -Ou -o foo.bcf`
#2263
jkbonfield
closed
4 weeks ago
1
Compiling on Centos 7.9 requires adding '-std=gnu99' to CFLAGS
#2262
Gullumluvl
closed
1 month ago
2
Ensure clean compilation with -Wformat -Wformat=2
#2261
daviesrob
closed
4 weeks ago
1
bcftools consensus always output "Applied 0 variants" and does not change the reference sequence.
#2260
shiro-kur
closed
3 weeks ago
1
target file required for bcftools roh analysis
#2259
vivekruhelaIIITD
closed
3 weeks ago
1
Remove the `*` ALT Allele Reporting From a g.vcf Before (or After) Genotyping
#2258
jon4thin
opened
1 month ago
1
validator mistakenly rejects decimals in FORMAT/QR
#2257
oliverdrechsel
closed
1 month ago
3
bcftools mpileup resulting in downstream unparsable vcf record with allele M
#2256
anscholes
opened
1 month ago
1
Improve documentation of mpileup adjust-MQ.
#2255
jkbonfield
closed
1 month ago
1
Installation failed
#2254
ShannonTown
closed
3 weeks ago
2
Error with prune plugin "prune.so: undefined symbol: vcfbuf_ld"
#2253
KevinABird
closed
3 weeks ago
1
Prevent bcftools sort from opening too many temporary files, and make it stable
#2252
daviesrob
closed
1 month ago
0
Fix 2249
#2251
jkbonfield
closed
1 month ago
0
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