User: Charlotte.Herzeel

Reputation:
140
Status:
Trusted
Location:
Belgium/Leuven/Imec
Website:
https://github.com/Exa...
Twitter:
@caherzee
Last seen:
2 months ago
Joined:
10 months, 1 week ago
Email:
C****************@imec.be

Posts by Charlotte.Herzeel

<prev • 10 results • page 1 of 1 • next >
0
votes
2
answers
1.2k
views
2
answers
Answer: A: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... Our article where we compare C++, Java, and Go for implementing elPrep has just been published by BMC Bioinformatics. This article describes the advantages and challenges we encountered in these languages when implementing a SAM/BAM tool and motivates why we ended up choosing Go for elPrep. See: ht ...
written 11 weeks ago by Charlotte.Herzeel140
0
votes
2
answers
1.2k
views
2
answers
Comment: C: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... Would you mind telling us which variant callers you are using that need indel realignment? Thanks. ...
written 6 months ago by Charlotte.Herzeel140
0
votes
2
answers
1.2k
views
2
answers
Comment: C: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... Thanks a lot for trying elPrep! We will look into indel realignment, but I can't promise we will implement this soon. ...
written 6 months ago by Charlotte.Herzeel140
0
votes
2
answers
1.2k
views
2
answers
Comment: C: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... The final version of our article was just published by PLOS One. See https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0209523 ...
written 6 months ago by Charlotte.Herzeel140
1
vote
2
answers
1.2k
views
2
answers
Answer: A: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... We are happy to announce that a preprint of our new paper describing elPrep 4 is now available. See https://t.co/u6h12mQPhx ...
written 8 months ago by Charlotte.Herzeel140
1
vote
2
answers
1.2k
views
2
answers
Comment: C: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... Hi, I am a bit confused about your remark. We tested elPrep a lot, including on data from SRA archives, but apart from optical duplicate marking, we haven’t encountered any issues because of QNAME fields. When elPrep is not able to recover tile information from the QNAME fields, it will skip optica ...
written 10 months ago by Charlotte.Herzeel140
1
vote
2
answers
1.2k
views
2
answers
Comment: C: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... Thanks! elPrep is indeed designed as a modular plug-in architecture where the implementation of SAM/BAM tools is separated from the engine that parallelises and merges their execution. We have extensive [documentation][1] and very much welcome contributions and suggestions for extending elPrep to su ...
written 10 months ago by Charlotte.Herzeel140
2
votes
2
answers
1.2k
views
2
answers
Comment: C: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... Yes, you are right. We have seen the same problem. elPrep currently only supports the Illumina format for optical duplicate marking, which is what GATK4 also supports by default. If you would like us to support other formats, please submit an issue on our [github][1] repository so we can discuss thi ...
written 10 months ago by Charlotte.Herzeel140
1
vote
2
answers
1.2k
views
2
answers
Comment: C: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto
... Hi, We only make assumptions about the read names (QNAME) for optical duplicate marking, as they have to encode the tile + coordinates. Is this what you mean? If not, could you provide more details, e.g. the error message you get? Thanks! ...
written 10 months ago by Charlotte.Herzeel140
21
votes
2
answers
1.2k
views
5 follow
2
answers
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
... Dear colleagues, We are happy to announce the release of elPrep 4.0.0, an open-source, drop-in replacement tool for GATK4/Picard/SAMtools for preparing SAM/BAM files for variant calling that produces identical results, while greatly improving computational performance. For more details, see the [el ...
bam sam sort markduplicates bqsr tool written 10 months ago by Charlotte.Herzeel140

Latest awards to Charlotte.Herzeel


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1387 users visited in the last hour