A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.
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Different pangolin lineages given variant caller #63
First, thank you for this great tool. I have a list of different pipelines to test, and yours is the only one that got installed and runs easily!
I ran your pipeline on my fastq files and in the results directory I got different fasta files, one for each VCF file as explained. All of them except for the lofreq resulted as a BA.2 lineage et the lofreq one was B.1.1.529.
Hi,
First, thank you for this great tool. I have a list of different pipelines to test, and yours is the only one that got installed and runs easily!
I ran your pipeline on my fastq files and in the results directory I got different fasta files, one for each VCF file as explained. All of them except for the lofreq resulted as a BA.2 lineage et the lofreq one was B.1.1.529.
How do I know which tool's results I should keep?
Thanks, Best