Genomic variants - SNPs and INDELs detection using GATK4 spark based tools.
Version 1

Workflow Type: Common Workflow Language
Stable

Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in

This is a proposed standard operating procedure for genomic variant detection using GATK4.

It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.

It uses Illumina RNASEQ reads and genome sequence.

Inputs

ID Name Description Type
sars_cov_2_reference_genome n/a n/a
  • File
sars_cov_2_reference_2bit_genome n/a n/a
  • File
rnaseq_left_reads n/a n/a
  • File
rnaseq_right_reads n/a n/a
  • File
sampleName n/a n/a
  • string

Steps

ID Name Description
index_reference_genome_with_bowtie2 n/a n/a
align_rnaseq_reads_to_genome n/a n/a
index_reference_genome_with_samtools n/a n/a
create_sequence_dictionary n/a n/a
update_read_group n/a n/a
sort_sam n/a n/a
mark_duplicates n/a n/a
split_alignments n/a n/a
index_split_alignments n/a n/a
call_plausible_haplotypes_and_detect_variants n/a n/a
filer_out_low_quality_variants n/a n/a
select_indels n/a n/a
select_snps n/a n/a

Outputs

ID Name Description Type
indels n/a n/a
  • File
snps n/a n/a
  • File

Version History

Version 1 (earliest) Created 17th Jun 2020 at 07:38 by Ambarish Kumar

Added/updated 2 files


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Views: 1099   Downloads: 58

Created: 17th Jun 2020 at 07:38

Last used: 25th Jun 2022 at 15:39

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