Request for support of Sentieon-Dedup

[asp8200]

Name of the tool

Sentieon Dedup

Tool homepage

https://support.sentieon.com/manual/usages/general/#dedup-algorithm

Tool description

The Dedup algorithm performs the marking/removing of duplicate reads.

Tool output

test.md.cram.metrics.zip

Log filename pattern

No response

Data suitable for MultiQC plot(s)

I imagine that the metrics from Sentieon-Dedup should be displayed pretty much like the corresponding metrics from GATK's Markduplicates.

Here is an example of how the first part of the metrics-file from Dedup may look:

#SentieonCommandLine: /opt/sentieon/sentieon-genomics-202112.06/libexec/driver -t 2 -i test.paired_end.sorted.bam -r genome.fasta --algo Dedup --score_info test.md.score --metrics test.md.cram.metrics test.md.cram
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
testN	0	2820	2	2	0	828	0	0.293617	3807

#HISTOGRAM
BIN	VALUE
1.0	0.999986
2.0	1.476740
3.0	1.704038
...

And here is the complete set of metrics from GATK's markduplicates for the same sample:

## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT test.bam --OUTPUT test.md.cram --METRICS_FILE test.md.cram.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Jun 16 09:17:57 GMT 2023

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
test	8601	721	82	523429	3876	0	0	0.38594

## HISTOGRAM	java.lang.Double
set_size	all_sets	non_optical_sets
1.0	721	721

Most interesting data for the General Stats table

No response

Before submitting

• I have included example data (zipped, not pasted) that can be used to write the module.

[asp8200]

MultiQC already contains support for three Sentieon DNAseq-modules but not Dedup. It was however already requested :

#1180

I plan to add the Dedup function here:

https://github.com/ewels/MultiQC/blob/master/multiqc/modules/sentieon/sentieon.py

And the Dedup function/module will probably be almost identical to the one for MarkDuplicates.

https://github.com/ewels/MultiQC/blob/master/multiqc/modules/picard/MarkDuplicates.py

In fact, I plan to just copy the MarkDuplicates module and adjust it for Sentieon 😆

[vladsavelyev]

Thank you again @asp8200 for raising the issue, contributing a test example and creating a PR!

We addressed this by supporting Sentieon by the Picard module directly, so we can easier expand to other Sentieon QC tools matching Picard tools: #2110

Hope that works. Please don't hesitate to leave comments or raise issues if anything got broken, or if you have other requests :)

[asp8200]

Thanks, @vladsavelyev. So I guess that will be released as part of v1.18, right? When do you reckon that will hit the streets?

[ewels]

Friday, if all goes to plan 🤞🏻