lofreq_call

Call variants from BAM file

--ref REF

Indexed reference fasta file. (default: None)

Option is required.

--in-bam IN_BAM

Path of the BAM/CRAM file. This option is required. (default: None)

Option is required.

--ign-vcf IGN_VCF [IGN_VCF ...]

Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by space (default: None)

--out OUT

Vcf output file. (default: None)

Option is required.

--num-threads NUM_THREADS

Number of threads per GPU. (default: 1)

--min-bq MIN_BQ

Skip any base with baseQ smaller than INT. (default: 6)

--min-alt-bq MIN_ALT_BQ

Skip alternate bases with baseQ smaller than INT. (default: 6)

--min-jq MIN_JQ

Skip any base with joinedQ smaller than INT. (default: 0)

--min-alt-jq MIN_ALT_JQ

Skip alternate bases with joinedQ smaller than INT. (default: 0)

--no-baq

Disable use of base-alignment quality (BAQ) (default: None)

--no-idaq

Don circumstances other than debugging) (default: None)

--del-baq

Delete pre-existing BAQ values, i.e. compute even if already present in BAM (default: None)

--no-ext-baq

Use extended BAQ (both computed on the fly if not already present in lb tag) (default: None)

--min-mq MIN_MQ

Skip reads with mapping quality smaller than INT. (default: 0)

--max-mq MAX_MQ

Cap mapping quality at INT. (default: 255)

--no-mq

Don (default: None)

--src-qual

Enable computation of source quality (default: None)

--def-nm-q DEF_NM_Q

If >= 0, then replace non-match base qualities with this default value. (default: -1)

--sig SIG

P-Value cutoff / significance level. (default: 0.01)

--bonf BONF

Bonferroni factor. INT (default: 1)

--min-cov MIN_COV

Test only positions having at least this coverage. (default: 1)

--illumina-1-3

Assume the quality is Illumina-1.3-1.7 encoded (default: None)

--use-orphan

Count anomalous read pairs (i.e. where mate is not aligned properly) (default: None)

--no-default-filter

Don calling variants (default: None)

--force-overwrite

Overwrite any existing output (default: None)

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)

--keep-tmp

Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.

--no-seccomp-override

Do not override seccomp options for docker (default: None).

--version

View compatible software versions.

--num-gpus NUM_GPUS

Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.

--gpu-devices GPU_DEVICES

GPU devices to use for a run. By default, all GPU devices will be used. To use specific GPU devices, enter a comma-separated list of GPU device numbers. Possible device numbers can be found by examining the output of the nvidia-smi command. For example, using --gpu-devices 0,1 would only use the first two GPUs.