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GAFL
Pipelines_Snakemake
wgs_gatk
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48b5111b
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48b5111b
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May 21, 2021
by
Jacques Lagnel
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update README
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{::options parse_block_html="true" /}
# WGS SNPs calling pipeline for Paired-end Illumina sequencing
## From raw fastq data to vcf file.
## Pipeline features:
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@@ -17,15 +16,8 @@
https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants
<div
class=
"panel panel-warning"
>
**Warning**
{: .panel-heading}
<div
class=
"panel-body"
>
!! For the reference fasta file, he reference definition line must not contain space or special character.
For the reference fasta file, he reference definition line must not contain space or special character.
</div>
</div>
## Snakemake features: fastq from csv file, config, modules, SLURM
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