ExaScience elprep issues

ExaScience / elprep

elPrep: a high-performance tool for analyzing sequence alignment/map files in sequencing pipelines.

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issues

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invalid BGZF file: does not end in proper EOF marker

#74 lucy-1n-the-ai opened 4 months ago
1
elprpe vcf-to-elsites dbSNP_156.vcf dbSNP_156.elsites [Killed]

#73 QifengSun opened 1 year ago
0
Use ASCIISet

#72 elliotwutingfeng opened 1 year ago
0
NO_COOR error when trying to index the output bam file

#71 ghost opened 1 year ago
0
build fails on ALMA linux 9

#70 ntm opened 1 year ago
0
Option to output realigned BAM file during --haplotypecaller step

#69 leonorpalmeira opened 1 year ago
0
elfasta-conversion error: bufio.Scanner: token too long

#68 desmodus1984 opened 1 year ago
6
Very low number of variants called by elprep in an heterozygous genome

#67 chklopp opened 1 year ago
0
feature: index output

#66 matthdsm opened 1 year ago
2
elprep merge: add input for intermediate files

#65 matthdsm opened 2 years ago
0
header tag differs between runs

#64 matthdsm opened 2 years ago
2
Add wiki page about "creating your own `sfm` script"

#63 matthdsm opened 2 years ago
3
`elprep split` output directory

#62 matthdsm closed 2 years ago
5
elprep5: gVCF does not match BAM read pileup

#61 splaisan closed 2 years ago
2
coverage vs vcf.gz size discrepancy

#60 desmodus1984 closed 2 years ago
4
Proper running using sam input file?

#59 desmodus1984 opened 2 years ago
1
vcf-to-elsites

#58 Mahmoudbassuoni closed 2 years ago
3
"exit status 2" error

#57 yanlolo opened 2 years ago
2
Variant calling using `sfm` does not adhere to thread limit

#56 matthdsm opened 3 years ago
13
Issue during build of v5.1.0

#55 matthdsm closed 3 years ago
3
GATK equivalency - version

#54 matthdsm closed 3 years ago
1
Comment: handling RG's in SFM

#53 matthdsm closed 3 years ago
4
[RFE] haplotypecaller: support for custom GVCF GQ slices

#52 ntm opened 3 years ago
1
sfm --haplotypecaller introduces duplicate lines in BAM

#51 ntm opened 3 years ago
2
exit status 2

#50 nmc-ei closed 3 years ago
6
Doing just variant calling /haplotypecaller? non-model organism no known-variant file for bqsr

#49 desmodus1984 opened 3 years ago
7
Add conda install suggestion, add badges

#48 matthdsm closed 3 years ago
0
Support for multiple input files

#47 matthdsm closed 3 years ago
5
BQSR filters out reads 'not in target region'

#46 pcostanza closed 3 years ago
2
Converting a dbsnp vcf to elsites uses a lot of resources

#45 pcostanza opened 3 years ago
3
Estimate RAM usage based on input filesize

#44 matthdsm opened 3 years ago
14
How to call population snps/indels?

#43 xiekunwhy closed 3 years ago
3
Is this a reasonable way to limit default threads used

#42 jbh-cas closed 3 years ago
3
More memory needed than samtools on 1CPU

#41 Juke34 closed 3 years ago
3
panic: interface conversion: interface {} is nil, not string

#40 Juke34 closed 3 years ago
2
Update README.md

#39 Juke34 closed 3 years ago
2
UMI's and duplicate marking

#38 matthdsm opened 4 years ago
1
elprep sfm run failed due to insufficient RAM

#37 babicjovana closed 4 years ago
1
Secondary .bai files

#36 babicjovana closed 4 years ago
1
Unclipped position not present in SAM alignment

#35 babicjovana closed 4 years ago
9
Does the command remove duplicates also does the marking of the duplicates?

#34 babicjovana closed 4 years ago
2
Encapsulate format conversions into elprep

#33 vladimirkovacevic closed 4 years ago
4
filter mismatches and or percentage identity?

#32 colindaven closed 3 years ago
1
How to control compression level of output?

#31 carlosmag closed 3 years ago
1
elprep sfm mode exits with out of Memory error

#30 ajayrv closed 4 years ago
9
Feature request: working with limits on VMEM

#29 chrisvanrun closed 4 years ago
2
Large amount of diskspace required

#28 chrisvanrun closed 4 years ago
6
Q: support for PacBio "native" format

#27 ptrebert closed 4 years ago
2
MapReduce markdup

#26 ghost closed 4 years ago
3
Compilation problems

#25 bvalot closed 5 years ago
1