Improvements - NVIDIA Docs

NVIDIA Docs Hub NVIDIA Clara Clara Parabricks v3.8.0 Improvements

Tools with new command line options

consensusreads:

--error-rate-pre-umi ERROR_RATE_PRE_UMI

Set the Phred-scaled error rate for an error prior to the UMIs being integrated. (default: 45)

--error-rate-post-umi ERROR_RATE_POST_UMI

The Phred-scaled error rate for an error post the UMIs have been integrated. (default: 40)

--min-input-base-quality MIN_INPUT_BASE_QUALITY

Ignore bases in raw reads that have Q below this value. (default: 10)

--min-consensus-base-quality MIN_CONSENSUS_BASE_QUALITY

Mask (make ‘N’) consensus bases with quality less than this threshold. (default: 2)

cnvkit:

The CNVkit implementation now supports the batch, autobin and coverage subcommands.

denovo mutation:

--run-partition

Divide the whole genome into multiple partition and run multiple processes at the same time, each on 1 partition.

germline:

--run-partition

Divide the whole genome into multiple partition and run multiple processes at the same time, each on 1 partition.

--no-alt-contigs

Get rid of output records for alternate contigs.

groupreadbyumi:

--min-map-q MIN_MAP_Q

Minimum mapping quality (default: 30)

haplotypecaller:

--run-partition

Divide the whole genome into multiple partition and run multiple processes at the same time, each on 1 partition.

--no-alt-contigs

Get rid of output records for alternate contigs.

human_par:

--use-GRCh37-regions

Use the pseudoautosomal regions for GRCh37 reference types. This flag should be used for GRCh37 and UCSC hg19 references. By default, GRCh38 regions are used.

rna_gatk:

--run-partition

Divide the whole genome into multiple partition and run multiple processes at the same time, each on 1 partition.

--no-alt-contigs

Get rid of output records for alternate contigs.

samtoolsmpileup:

--anomalous-reads

Do not discard anomalous read pairs.

--output-mq

Output mapping quality.

--output-bp

Output base positions on reads.

smoove:

--exclude-bed-file

Optional bgzip-compressed/tabix-indexed BED file containing the set of regions to exclude.

umi_fgbio:

--min-map-q MIN_MAP_Q

Minimum mapping quality. (default: 30)

--error-rate-pre-umi ERROR_RATE_PRE_UMI

The Phred-scaled error rate for an error prior to the UMIs being integrated. (default: 45)

--error-rate-post-umi ERROR_RATE_POST_UMI

The Phred-scaled error rate for an error post the UMIs have been integrated. (default: 40)

--min-input-base-quality MIN_INPUT_BASE_QUALITY

Ignore bases in raw reads that have Q below this value. (default: 10)

--min-consensus-base-quality MIN_CONSENSUS_BASE_QUALITY

Mask (make ‘N’) consensus bases with quality less than this threshold. (default: 2)

vcfqcbybam:

--output-mq

Output mapping quality.

--output-bp

Output base positions on reads.

General

Added support for A10, A30, A40, A6000 GPUs for all tools in Clara Parabricks. Visit the Deepvariant documentation page for more details.

Improved tumor-only calling in LoFreq.

Added end-to-end support for germline on Hopper.

Improved CNNScoreVariants tool.

Added multi-TSV annotation database support.

Added consequence calling using bcftools 'csq' option.

Speedup in reading and writing VCF files.

Add mapquality, basequality and fwd/rev alleles to summary in vcfqcbybam.

Improve float comparison in vcfdiff.

Add two sample support to votebasedvcfmerger.

Update CNVKIT to v0.9.9.

bam2fq no longer requires a reference file if BAM input is used.

haplotypecaller now uses multiple CPUs to process multiple partitions.