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samtools
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hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
http://samtools.github.io/hts-specs/
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#795
jmarshall
closed
2 days ago
1
Set off example tabular environment with the usual spacing [formatting]
#794
jmarshall
opened
2 days ago
1
vcf: VCF 4.5 text for LAA field flows into example
#793
zaeleus
opened
2 days ago
0
VCF 4.4: clarification on CNVs with position 0
#792
ctsa
closed
2 days ago
6
VCFv4.5 gVCF example malformed
#791
d-cameron
opened
2 weeks ago
0
LGL and LGP type incorrect
#790
d-cameron
opened
2 weeks ago
0
Clarify SVCLAIM for deletion bridges
#789
ctsa
closed
1 week ago
5
Fix CRAM pseudocode for handling BAM mapped flag (PR #788)
#788
jkbonfield
closed
4 weeks ago
1
[Improvement] BAM file format, optional strandedness field in header for RNA-seq
#787
rLannes
closed
3 weeks ago
8
0-based coordinate system error in sam spec?
#786
jacobscgc
closed
1 month ago
2
MM tag preferred format for TAPS data
#785
jamesbaye
opened
1 month ago
1
INFO/END should not be deprecated
#784
pd3
opened
1 month ago
14
INFO CIPOS Number=2xA
#783
rkimoakbioinformatics
opened
1 month ago
0
Add subtitles noting VCFv4.[1-4].pdf have been superseded by later versions
#782
jmarshall
opened
1 month ago
1
vcf: VCF 4.5 gVCF example has off-by-one errors
#781
zaeleus
opened
1 month ago
0
Using ChaCha20-Poly1305 for encryption is NOT FIPS140-3 compliant and not justified and is considered unprotected plaintext
#780
mmokrejs
opened
1 month ago
3
BED "chrom" field regex is inconsistent with existing practice
#779
EricR86
opened
2 months ago
5
FORMAT field CICN and its relation to CN field
#778
vasudeva8
opened
2 months ago
0
Number, type and description on FORMAT not in sync with List of changes
#777
vasudeva8
opened
2 months ago
0
Update base modification test files to use the final MM/ML tags
#776
jmarshall
closed
2 months ago
1
fix discrepancy of empty bed files
#775
kloetzl
opened
3 months ago
5
VCF format: correct representation of complex indels and MNPs
#774
marc-sturm
closed
3 months ago
5
Add ID subfield to VCF v4.3 test file's structured header
#773
jmarshall
opened
3 months ago
0
vcf: Invalid unstructured header line in VCF 4.3 example `complexfile_passed_000.vcf`
#772
zaeleus
opened
4 months ago
2
refget: v2 spec for Range header errors does not align with typical usage
#771
davidlougheed
opened
4 months ago
0
VCFv4.5 RC2
#770
d-cameron
closed
3 months ago
4
VCF4.4 SVLEN requirement across different variant representations
#769
tcezard
opened
5 months ago
6
Add a LICENSE.md file for the various test files.
#768
jkbonfield
opened
5 months ago
5
VCF Draft 4.5 and Modified Bases
#767
cjw85
opened
5 months ago
29
Questions about third-party use of test data
#766
athos
opened
5 months ago
6
CSI file is BGZF compressed but this is not mentioned in the CSV1 spec
#765
bguo068
opened
5 months ago
2
Fix a typo, it should be CN, not CICN
#763
pd3
closed
5 months ago
0
bcf: First phasing indicators not set in genotype (GT) value examples
#762
zaeleus
closed
5 months ago
0
Fix minor typos in the CRAM tag type lists (PR #761)
#761
jkbonfield
closed
6 months ago
1
vcf: Handling structured header records with missing IDs in VCF 4.1/4.2
#760
zaeleus
closed
3 months ago
1
SA tag CIGAR format
#759
jo-mc
closed
6 months ago
0
VCF 4.5 Future of VCF scaling improvements
#758
d-cameron
closed
5 months ago
29
cram: Inconsistent descriptions of auxiliary tag types
#757
athos
closed
6 months ago
1
Is there a semantic difference between GT=./. and GT=0/0 + GQ=0 ?
#756
yfarjoun
closed
3 months ago
15
How to retrieve the primary alignment for secondary and supplementary reads
#755
nh13
closed
2 months ago
9
Document CRAM FP is delta-encoded
#754
jkbonfield
closed
7 months ago
3
Add SAM recommendation of MAPQ=0 for unmapped reads
#753
jkbonfield
opened
8 months ago
6
Recommend 1bp SEQ with QUAL="*" as quality-unavailable.
#752
jkbonfield
opened
8 months ago
1
Trivial removal of duplicate tag in SAM test data
#751
jkbonfield
closed
7 months ago
0
SVCLAIM: VCF4.4 and backward compatibility with VCF4.3
#750
tcezard
closed
8 months ago
1
cram: interpretation of "unmapped" flag in a pseudocode seems incorrect
#749
athos
closed
4 weeks ago
2
is `*` better than `\*`?
#748
zhitian-wu
closed
10 months ago
1
CRAM: Need to improve feature positions description
#747
daviesrob
closed
7 months ago
1
FAIRsharing Record Query - BED format
#746
allysonlister
opened
10 months ago
0
Local Alleles (PR #434) applied to VCFv4.4
#745
jmarshall
closed
9 months ago
4
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