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broadinstitute
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GATK-for-Microbes
BSD 3-Clause "New" or "Revised" License
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#30
knokknok
opened
10 months ago
0
Docker independent pipeline?
#29
Guan06
opened
2 years ago
2
test script fails because ShiftFasta command is missing
#28
kxw116
opened
3 years ago
1
skipping the revert sam and sam-to-fastq steps for cases where we start with bam file
#27
bhanugandham
closed
3 years ago
0
Skip revertsam and samtofastq when the input is bam file
#26
bhanugandham
closed
3 years ago
0
Script for merging bed files
#25
sophiegr02
closed
3 years ago
0
Allow users to custom set the memory for the RevertSam task in MicrobialGenomePipeline
#24
jason-cerrato
opened
3 years ago
0
added gatk-microbial jar and shiftfasta jars to input json
#23
bhanugandham
closed
3 years ago
0
How to build gatk-micobialmode.jar?
#22
garlandcrow
closed
3 years ago
4
test with recover-all-branches M2 arg
#21
bhanugandham
opened
3 years ago
0
Rosalind exercises to be reviewed
#20
sophiegr02
closed
3 years ago
0
remove the hard coded override for shift fasta
#19
ahaessly
closed
3 years ago
0
added wdl to generate frequency of zmw occurances
#18
bhanugandham
closed
3 years ago
0
Ah shift bool
#17
ahaessly
closed
3 years ago
0
Exclude the filtered variants from the filtered.vcf output file
#16
bhanugandham
opened
3 years ago
0
Add a task for Terra UI to hide optional json outputs
#15
bhanugandham
opened
3 years ago
0
Explain the three output bamouts in documentation
#14
bhanugandham
opened
3 years ago
0
Make shift fasta optional
#13
bhanugandham
closed
3 years ago
0
Add an option in the wdl to prefix output files with sample_name
#12
bhanugandham
opened
3 years ago
0
Add joint calling as an option to the pipeline
#11
bhanugandham
opened
3 years ago
1
Generate RTG vcfeval summary.txt file as an output concordance wdl
#10
bhanugandham
opened
3 years ago
1
Revert "add flag for circular reference (#8)"
#9
bhanugandham
closed
3 years ago
1
add flag for circular reference
#8
ahaessly
closed
3 years ago
0
Ah fix bamout
#7
ahaessly
closed
3 years ago
0
Ah concordance
#6
ahaessly
closed
3 years ago
0
adding run date readgroup
#5
bhanugandham
closed
3 years ago
0
wdl for RTG comparison
#4
ahaessly
closed
3 years ago
0
added bamout to inputs json and removed the max-mnp-distance argument
#3
bhanugandham
closed
4 years ago
0
Bg add bamout
#2
bhanugandham
closed
4 years ago
0
Ah- initial wdl
#1
ahaessly
closed
4 years ago
0