MorrellLAB sequence_handling issues

MorrellLAB / sequence_handling

A series of scripts to automate sequence workflows

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issues

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add file extension

#53 Luis-WP-Arge closed 11 months ago
0
Filter_genotypes_fix

#52 EDitt closed 3 years ago
0
changed variable in output echo statement

#51 EDitt closed 3 years ago
1
Annotation figs

#50 EDitt closed 3 years ago
1
Temp

#49 EDitt closed 4 years ago
0
parallel long argument problem fixed

#48 ntakebay closed 4 years ago
0
Non-PBS parallelizing over regions for Haplotype_Caller, Genomics_DB_Import and Genotype_GVCFs

#47 ntakebay closed 4 years ago
0
A script for breaking up WGS data into smaller intervals at N strings

#46 EDitt closed 4 years ago
0
Change quotation around outFlag variable

#45 EDitt closed 4 years ago
1
Nanopore Adapter Trimming - not iterating

#44 pmorrell opened 4 years ago
0
Error message with NP_SAM_Processing

#43 pmorrell closed 4 years ago
0
sequence handling workflow numbers

#42 pmorrell closed 5 years ago
1
Check .g.vcf file is indexed

#41 ChaochihL closed 4 years ago
1
Edited checkVersion function in utils.sh

#40 EDitt closed 4 years ago
1
GATK4 can be used, It can be ran without PBS.

#39 ntakebay closed 5 years ago
0
'python-epd/1.5.2' needs to be updated to current version in Config file

#38 fervet01 closed 4 years ago
0
Options to Help With GATK HaplotypeCaller Making False Negative Errors

#37 TomJKono closed 4 years ago
2
Quality_Assessment fails to report the correct read length

#36 Aerin13 closed 6 years ago
3
Indel realignment parameters

#35 ChaochihL closed 6 years ago
1
Add check for reference.dict file required for HaplotypeCaller

#34 ChaochihL closed 6 years ago
1
Quality_Assessment outputs incorrect read depth when read length is variable

#33 Aerin13 closed 7 years ago
0
Quality Assessment not using alternate samples specified

#32 ChaochihL closed 7 years ago
2
Add Samtools version to Config file

#31 fervet01 closed 7 years ago
1
Truncated Files with Picard Handler

#30 TomJKono closed 7 years ago
1
SAM_Processing Output does not feed nicely into GATK

#29 Aerin13 closed 7 years ago
1
Paired end FASTQ have differed numbers of reads after adapter trimming

#28 pmorrell closed 7 years ago
1
sample_list_generator.sh changes

#27 Aerin13 closed 7 years ago
0
Inputting a gziped reference

#26 Aerin13 closed 7 years ago
1
Coverage Mapping Issue

#25 ChaochihL closed 7 years ago
2
SAM Processing Picard - Optional BAI files

#24 ChaochihL closed 8 years ago
0
Config file changes needed

#23 pmorrell closed 7 years ago
1
clarifying Config setup

#22 pmorrell closed 7 years ago
2
Running sequence_handling from not inside sequence_handling directory

#21 Aerin13 opened 8 years ago
0
Paired-end Quality Trimming

#20 Aerin13 closed 8 years ago
0
Coverage_Mapping.sh

#19 ChaochihL closed 8 years ago
0
Error in naming of processed BAM samples

#18 ChaochihL closed 8 years ago
1
add the step to do demultiplex for GBS data

#17 lilei1 opened 8 years ago
3
Quality_Assessment.sh error

#16 ChaochihL closed 8 years ago
4
Read mapping walltime increase

#15 ChaochihL closed 8 years ago
0
Renamed variable to match naming scheme

#14 mojaveazure closed 8 years ago
0
Move with_config into master

#13 mojaveazure closed 8 years ago
0
Specify Platform in comments

#12 ChaochihL closed 8 years ago
1
Common Config File

#11 ChaochihL closed 8 years ago
2
A warning in "6_SAM_Processing_SAMTools.sh"

#10 lilei1 closed 8 years ago
0
a bug in "Helper_Scripts/plot_seqqs.R"

#9 lilei1 closed 8 years ago
1
A bug in Line 173 of 4_Quality_Trimming.sh

#8 lilei1 closed 8 years ago
1
SAMPLE_INFO is not clear enough in 3_Read_Depths.sh

#7 lilei1 closed 8 years ago
0
update script names in recommended workflow

#6 pmorrell closed 8 years ago
1
add order for each script

#5 lilei1 closed 8 years ago
0
Line 66 in "read_counts.sh" should be revised

#4 lilei1 closed 8 years ago
0