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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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Problem with specifying filtering expression v1.21
#2322
reshu23
opened
2 days ago
0
Majority of SNPs have allele frequency = 0.000000
#2321
ryanskiba
opened
3 days ago
0
bcftools view -m 2 -M 2 referencePanel.vcf.gz（SV and SNP）
#2320
SunWinner01
opened
4 days ago
2
Filter a gene list including intergenic regions
#2319
ccbruels
opened
1 week ago
2
bcftools: command does not work correctly. Can you help me?
#2318
jhownatan1
closed
4 days ago
3
`bcftools norm` can not handle insertion-breakend entries with fasta reference (VCF4.3+)
#2317
Nicolai-vKuegelgen
closed
3 days ago
1
`bcftools consensous` fails to write to GCP
#2316
Ieremie
opened
1 week ago
0
Consensus of ALTs only without genotypes in file
#2315
schorlton-bugseq
opened
1 week ago
2
cmp_vector_strings() in filter.c complains that nvalues!=str_value.l for VCF lines missing the GT format
#2314
freeseek
closed
6 days ago
1
Error: bcftools csq --- splice_build_hap: Assertion `splice->tr->beg <= rbeg' failed.
#2313
sbgonenc
opened
2 weeks ago
0
bcftools header check err
#2312
xiucz
closed
6 days ago
3
seg fault for reheader -o
#2311
Ahuiting
opened
3 weeks ago
3
How to Generate Haplotype 1 and 2 FASTA Files Using Phased VCF from HiPhase
#2310
ClarenceHsiang
opened
4 weeks ago
1
Bcftools view——locate problematic genotype in GT field
#2309
Lloyd-LiuSiyi
opened
4 weeks ago
6
Trying to understand mpileup output format
#2308
anderspitman
closed
1 week ago
4
Fix a few warnings and ensure polysomy is built in the CI tests
#2307
daviesrob
closed
3 weeks ago
0
'annotate' error message when trying to put a Float into an 'Number=A,type=Integer' INFO
#2306
Gullumluvl
closed
3 weeks ago
1
Fix gmake 4.4 "pattern recipe did not update peer target" warnings
#2305
daviesrob
closed
1 month ago
1
Heterozygocity missing
#2304
cottonrnr
closed
1 month ago
2
Convert missing single dot to "./."?
#2303
bbimber
closed
3 weeks ago
2
bcftools annotate - tag ID not defined
#2302
ValentinaPeona
opened
1 month ago
3
bcftools call empty output with -o
#2301
niederhuth
closed
1 month ago
3
Can we use bcftools to create genome based on cram file
#2300
HelloWorldLTY
closed
1 month ago
1
Filtering out indels but keeping invariant sites
#2299
ja-Reeve
closed
1 month ago
1
Add support for matching VCF lines by ID
#2298
pd3
closed
1 month ago
0
Issue with bcftools annotate
#2297
HVHunt
opened
1 month ago
1
Make --write-index work with concat with vcf (version 2)
#2296
whitwham
closed
1 month ago
0
Warning: fewer CSQ fields than expected
#2295
kuaileshizuihao
closed
1 month ago
1
bcftools csq: Change chromosome name requirement.
#2294
niederhuth
opened
1 month ago
1
Error "Failed to read from standard input: unknown file type" with Gzipped BAM Files
#2293
Silvia-lme
opened
1 month ago
1
Sampling frequency field not found in the header. Please check the header fields.
#2292
wahibalkamat2
closed
1 month ago
1
BCFtools norm dropping duplicates options: is -d none equivalent to -d exact and -D ?
#2291
davidjakubosky
closed
1 month ago
1
Is BCFtools norm guaranteed to maintain sort order?
#2290
davidjakubosky
closed
1 month ago
1
CI improvements
#2289
jkbonfield
closed
1 month ago
1
Fix cut and paste errors in writing the get_data.sh script.
#2288
jkbonfield
closed
1 month ago
1
How to populate Fisher test annotation
#2287
pd3
opened
1 month ago
1
bcftools concat segfault if VCF files contain only headers
#2286
dpryan79
closed
1 month ago
3
Bcftools merge
#2285
desmodus1984
closed
1 month ago
1
`--output-type u --write-index=tbi` writes csi index
#2284
fellen31
closed
1 month ago
1
Make --write-index work for concat with vcf (needs htslib#1839)
#2283
whitwham
closed
1 month ago
1
Make the mpileup BAM_CREF_SKIP filter optional.
#2282
jkbonfield
opened
2 months ago
0
Remove the mpileup BAM_CREF_SKIP filter.
#2281
jkbonfield
opened
2 months ago
2
Document / Improve / Polish / Fix --indels-2.0
#2280
jkbonfield
opened
2 months ago
3
split-vep AF
#2279
andrew2k
closed
1 month ago
1
Bcftools view error about an invalid tag "1000gALT", how do I fix this?
#2278
PVlasov93
closed
1 month ago
1
Significant difference between IDV and AD when calling certain RNA-seq indels with mpileup
#2277
luyh-xp
opened
2 months ago
8
Variable expansion issue with +setGT? [$VARIABLE-] isn't working...
#2276
goeckeritz
opened
2 months ago
1
Work around an incompatibility between Perl and clang warnings.
#2275
jkbonfield
closed
2 months ago
1
Reapply previous Makefile dependency fix
#2274
jmarshall
closed
2 months ago
0
annotate add INFO/tag form CHROM-POS-REF-ALT
#2273
user-tq
opened
2 months ago
0
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