From 3dd53a8af63f66bd2e9d64693670b48b6e1c742c Mon Sep 17 00:00:00 2001 From: Kishwar Date: Tue, 15 Mar 2022 22:58:34 -0700 Subject: [PATCH] parameter and methods update --- docs/misc/pepper_methods.md | 17 +++++++++++++- docs/usage/usage_and_parameters.md | 36 +++++++++++++++++------------- 2 files changed, 37 insertions(+), 16 deletions(-) diff --git a/docs/misc/pepper_methods.md b/docs/misc/pepper_methods.md index 50d87c3f..b869a0ea 100644 --- a/docs/misc/pepper_methods.md +++ b/docs/misc/pepper_methods.md @@ -71,6 +71,21 @@ iii) `find_candidates`: This step takes the predictions of the previous step to

* All variants are used for haplotagging with margin. + +Update in `r0.8`: From this version, we split the SNP and INDEL candidates into two VCFs to enable SNP and INDEL calling separately with DeepVariant. +The PEPPER output VCFs are: +```bash +PEPPER_VARIANT_FULL.vcf.gz : Contails all variants reported by PEPPER. +PEPPER_VARIANT_OUTPUT_PEPPER.vcf.gz: Contains only the variants that are found high-quality in PEPPER and will not be re-gotyped with DeepVariant. +PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_INDEL.vcf.gz: Contains INDEL candidate variants that will be re-genotyped with DeepVariant. +PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_SNPs.vcf.gz: Contains SNP candidate variants that will be re-genotyped with DeepVariant. +PEPPER_VARIANT_OUTPUT_VARIANT_CALLING.vcf.gz: Contains all candidate variants (SNPs + INDELs) that will be re-genotyped with DeepVariant. +``` + +For Oxford Nanopore variant calling, we now use: +* DeepVariant `rows` mode that uses INDEL realignment for calling candidate variants from `PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_INDEL.vcf.gz`. +* DeepVariant `none` mode that uses SNP calling for calling candidate variants from `PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_SNPs.vcf.gz`. + ### Step 2: Margin [Haplotagging reads] Margin uses the read-based evidence of linkage between heterozygous variant sites to find the most likely assignment of reads and alleles to haplotypes. The tool first selects a set of high-quality primary reads and variants for use in the initial phasing workflow. @@ -111,7 +126,7 @@ The following parameters are used to select reads: * `phase.maxDepth`: reads are downsampled to an expected depth of this parameter. Longer reads are preferentially selected during downsampling. ### Step 3: DeepVariant -DeepVariant re-genotypes the candidates proposed by `PEPPER-HP` using reads haplotagged by `Margin`. We use the following features for DeepVariant: +DeepVariant re-genotypes the candidates proposed by `PEPPER` using reads haplotagged by `Margin`. We use the following features for DeepVariant:

DeepVariant summary

diff --git a/docs/usage/usage_and_parameters.md b/docs/usage/usage_and_parameters.md index f0a3023e..f683b7b6 100644 --- a/docs/usage/usage_and_parameters.md +++ b/docs/usage/usage_and_parameters.md @@ -103,18 +103,24 @@ run_pepper_margin_deepvariant call_variant --help | --margin_phase_model | String | Path to a custom margin model. | ### Parameters for DeepVariant -| Parameter | Type | Description | -|------------------------------|---------|------------------------------------------------------------------------------------| -| --dv_model | String | Path to a custom DeepVariant model. | -| --dv_alt_aligned_pileup | String | DeepVariant alt_align_pileup used for make_examples. [none, rows, diff_channels] | -| --dv_realign_reads | String | If true then local read alingment will be performed. [set: true/false] | -| --dv_partition_size | String | DeepVariant partition_size used for make_examples. | -| --dv_min_mapping_quality | Integer | DeepVariant minimum mapping quality. | -| --dv_min_base_quality | Integer | DeepVariant minimum base quality. | -| --dv_sort_by_haplotypes | String | If true then haplotype sorting will be used. [set: true/false] | -| --dv_parse_sam_aux_fields | String | If true then auxiliary field parsing is enabled. [set: true/false] | -| --dv_add_hp_channel | String | If true then hp channel will be added. [set: true/false] | -| --dv_use_hp_information | String | If true then hp information will be properly used. [set: true/false] | -| --dv_use_multiallelic_mode | String | If true multiallelic model will be used during post-processing. [set: true/false] | -| --dv_vsc_min_fraction_indels | String | DeepVariant minimum vsc fraction for indels. | -| --dv_vsc_min_fraction_snps | String | DeepVariant minimum vsc fraction for snps. | +| Parameter | Type | Description | +|-------------------------------|---------|----------------------------------------------------------------------------------------------------------| +| --dv_model | String | Path to a custom DeepVariant model. If set, then this model will be used for both SNP and INDEL calling. | +| --dv_model_snp | String | Custom DeepVariant model for SNP calling. | +| --dv_model_indel | String | Custom DeepVariant model for INDEL calling. | +| --dv_alt_aligned_pileup | String | alt_align_pileup used for make_examples of --dv_model parameter. [none, rows, diff_channels] | +| --dv_alt_aligned_pileup_snp | String | alt_align_pileup used for make_examples of --dv_model_snp parameter. [none, rows, diff_channels] | +| --dv_alt_aligned_pileup_indel | String | alt_align_pileup used for make_examples of --dv_model_indel parameter. [none, rows, diff_channels] | +| --dv_pileup_image_width | String | DeepVariant image width. [none, rows, diff_channels] | +| --dv_realign_reads | String | If true then local read alingment will be performed. [set: true/false] | +| --dv_partition_size | String | DeepVariant partition_size used for make_examples. | +| --dv_min_mapping_quality | Integer | DeepVariant minimum mapping quality. | +| --dv_min_base_quality | Integer | DeepVariant minimum base quality. | +| --dv_vsc_min_fraction_indels | String | DeepVariant minimum vsc fraction for indels. | +| --dv_vsc_min_fraction_snps | String | DeepVariant minimum vsc fraction for snps. | +| --dv_sort_by_haplotypes | String | If true then haplotype sorting will be used. [set: true/false] | +| --dv_parse_sam_aux_fields | String | If true then auxiliary field parsing is enabled. [set: true/false] | +| --dv_add_hp_channel | String | If true then hp channel will be added. [set: true/false] | +| --dv_use_hp_information | String | If true then hp information will be properly used. [set: true/false] | +| --dv_use_multiallelic_mode | String | If true multiallelic model will be used during post-processing. [set: true/false] | +