Update README.md

WES/README.md

@@ -35,11 +35,6 @@ Below the workflow and commands used:
 ```
 - gatk Mutect2 -I SampleID.disambiguatedSpeciesA.bam.sorted.bam -O Mutect2_raw_call_SampleID_exome_refseq_light.vcf.gz -R GRCh38.p13.genome.fa -L exome_light.bed -G StandardMutectAnnotation -OVI true -OVM true -ip 50
 - gatk FilterMutectCalls -R GRCh38.p13.genome.fa -V Mutect2_raw_call_SampleID_exome_refseq_light.vcf.gz -O Mutect2_raw_call_SampleID_exome_refseq_light_filtered.vcf.gz
-- bcftools view -i 'FORMAT/DP>10' Mutect2_raw_call_SampleID_exome_refseq_light_filtered.vcf.gz -O z > Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10.vcf.gz
-- bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t[%DP\t]\t[%AD\t]\t[%AF\t]\t[%GT\t]\n' Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10.vcf.gz > Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10_fields.txt
-- bcftools view -f PASS Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10.vcf.gz -O z > Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10_PASS.vcf.gz
-- bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t[%DP\t]\t[%AD\t]\t[%AF\t]\t[%GT\t]\n' Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10_PASS.vcf.gz > Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10_PASS_fields.txt
-
 ```
 
 # Annotation #