wgs_analysis

Participants in the hackathon (14):

                            Andreia Amaral

                           Juliana Menezes
                           Pedro Sá
                           
                           Lucio Marcello 
                           
                           Leila Mansouri-CRG
                           
                           Suzanne Jin|BovReg|CRG
                           
                           Meenu Bhati | BovReg | ETH
                           
                           Kylie Munyard Curtin Uni/ Fr-AgENCODE
                           
                           Cervin Guyomar - FAANG - INRAE Toulouse
                           
                           Zeinab Manzari 
                           
                           Phanindra-SLU-FAANG
                           
                           Philippe BARDOU
                           
                           Alexandre Gilardet 
                           
                           Jose Espinosa

WORKFLOW

Tools for the workflow and manual instructions

PICARD

1- create genome dictionary

java -jar /data/software/picard/build/libs/picard.jar CreateSequenceDictionary \ R=GCF_002310715.1_ASM231071v1_genomic.fna \ O=rGCF_002310715.1_ASM231071v1_genomic.dict

2- java -jar /data/software/picard/build/libs/picard.jar MarkDuplicates
I=E2_alnRG_sorted.bam
O=E2_alnRGsorted_duplicates_removed.bam
M=E2_alnRGsorted_duplicates_removed_dup_metrics.txt
REMOVE_SEQUENCING_DUPLICATES=true

3- After having all individual VCFs merged them in a single VCF

java -jar /data/software/picard/build/libs/picard.jar MergeVcfs
I=E1_output_filtered.vcf.gz
I=E2_output_filtered.vcf.gz
O=E12output_variants.vcf.gz

SAMTOOLS

1. Genome indexing

samtools faidx GCF_002310715.1_ASM231071v1_genomic.fna

2. convert SAM to BAM samtools view -S -b E2-aln_1223.sam.sam > E2-aln_1223.bam

GATK

1- Variant calling

gatk --java-options "-Xmx4g" HaplotypeCaller
-R GCF_002310715.1_ASM231071v1_genomic.fna
-I E2_alnRGsorted_duplicates_removed.bam
-O E2_output.vcf.gz
-bamout E2_bamout.bam

2. Variant filter

   gatk VariantFiltration
   -R GCF_002310715.1_ASM231071v1_genomic.fna
   -V E2_output.vcf.gz
   -O E2_output_filtered.vcf.gz
   --filter-name "my_filter1"
   --filter-expression "QUAL < 0 || DP<10.0 || MQ < 30.00 || SOR > 10.000 || QD < 2.00 || QD> 5.00|| FS > 200.000 || ReadPosRankSum < -20.000 || ReadPosRankSum > 20.000"