From 3dd53a8af63f66bd2e9d64693670b48b6e1c742c Mon Sep 17 00:00:00 2001
From: Kishwar
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] | +