Changed scratch3 to scratch

hbctraining · May 8, 2024 · aeed707 · aeed707
1 parent 24eec38
commit aeed707
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/lessons/07_variant_calling.md b/lessons/07_variant_calling.md
@@ -277,10 +277,10 @@ Next, we need to add our variables:
 REFERENCE_SEQUENCE=/n/groups/hbctraining/variant_calling/reference/GRCh38.p7.fa
 REFERENCE_DICTIONARY=`echo ${REFERENCE_SEQUENCE%fa}dict`
 NORMAL_SAMPLE_NAME=syn3_normal
-NORMAL_BAM_FILE=/n/scratch3/users/${USER:0:1}/${USER}/variant_calling/alignments/${NORMAL_SAMPLE_NAME}_GRCh38.p7.coordinate_sorted.bam
+NORMAL_BAM_FILE=/n/scratch/users/${USER:0:1}/${USER}/variant_calling/alignments/${NORMAL_SAMPLE_NAME}_GRCh38.p7.coordinate_sorted.bam
 TUMOR_SAMPLE_NAME=syn3_tumor
-TUMOR_BAM_FILE=/n/scratch3/users/${USER:0:1}/${USER}/variant_calling/alignments/${TUMOR_SAMPLE_NAME}_GRCh38.p7.coordinate_sorted.bam
-VCF_OUTPUT_FILE=/n/scratch3/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_${NORMAL_SAMPLE_NAME}_${TUMOR_SAMPLE_NAME}_GRCh38.p7-raw.vcf
+TUMOR_BAM_FILE=/n/scratch/users/${USER:0:1}/${USER}/variant_calling/alignments/${TUMOR_SAMPLE_NAME}_GRCh38.p7.coordinate_sorted.bam
+VCF_OUTPUT_FILE=/n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_${NORMAL_SAMPLE_NAME}_${TUMOR_SAMPLE_NAME}_GRCh38.p7-raw.vcf
 ```
 
 <details>
@@ -408,10 +408,10 @@ module load gatk/4.1.9.0
 REFERENCE_SEQUENCE=/n/groups/hbctraining/variant_calling/reference/GRCh38.p7.fa
 REFERENCE_DICTIONARY=`echo ${REFERENCE_SEQUENCE%fa}dict`
 NORMAL_SAMPLE_NAME=syn3_normal
-NORMAL_BAM_FILE=/n/scratch3/users/${USER:0:1}/${USER}/variant_calling/alignments/${NORMAL_SAMPLE_NAME}_GRCh38.p7.coordinate_sorted.bam
+NORMAL_BAM_FILE=/n/scratch/users/${USER:0:1}/${USER}/variant_calling/alignments/${NORMAL_SAMPLE_NAME}_GRCh38.p7.coordinate_sorted.bam
 TUMOR_SAMPLE_NAME=syn3_tumor
-TUMOR_BAM_FILE=/n/scratch3/users/${USER:0:1}/${USER}/variant_calling/alignments/${TUMOR_SAMPLE_NAME}_GRCh38.p7.coordinate_sorted.bam
-VCF_OUTPUT_FILE=/n/scratch3/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_${NORMAL_SAMPLE_NAME}_${TUMOR_SAMPLE_NAME}_GRCh38.p7-raw.vcf
+TUMOR_BAM_FILE=/n/scratch/users/${USER:0:1}/${USER}/variant_calling/alignments/${TUMOR_SAMPLE_NAME}_GRCh38.p7.coordinate_sorted.bam
+VCF_OUTPUT_FILE=/n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_${NORMAL_SAMPLE_NAME}_${TUMOR_SAMPLE_NAME}_GRCh38.p7-raw.vcf
 
 # Run MuTect2
 gatk Mutect2 \