Genomic variants - SNPs and INDELs detection using GATK4.
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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
rnaseq_left_reads n/a n/a File
rnaseq_right_reads n/a n/a File
indices_folder n/a n/a Directory

Steps

ID Name Description
index_reference_genome_with_bowtie2
align_rnaseq_reads_to_genome
index_reference_genome_with_samtools
create_sequence_dictionary
update_read_group
mark_duplicates
split_alignments
index_split_alignments
call_plausible_haplotypes_and_detect_variants
filer_out_low_quality_variants
select_indels
select_snps

Outputs

ID Name Description Type
indels n/a n/a File
snps n/a n/a File
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Views: 80   Downloads: 6

Created: 17th Jun 2020 at 07:11

Last used: 11th Aug 2020 at 18:35

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