Running and Verification

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to go to the test case directory:

   cd /path/to/DELLY/CASE

3. Run the following command to decompress the test case package:

   gzip -d B17NC_R1.fq.gz

4. Run the following command to create an index file:

   bwa index -a bwtsw hg19.fa

5. Run the following command to create a .sam file:

   bwa mem -t 96 hg19.fa B17NC_R1.fastq > bwa.sam

6. Run the following commands to create a .bam file and process it:

   samtools view -bS bwa.sam > B17NC_R1.bam
   samtools sort -@96 B17NC_R1.bam -o B17NC_R1.sort.bam
   samtools index -@96 B17NC_R1.sort.bam B17NC_R1.sort.bam.bai

7. Run the following script to copy the .bam file to simulate the running of multiple samples at the same time:

   #!/bin/bash
   for varible1 in {1..127}
   do
   cp B17NC_R1.sort.bam B17NC_R1${varible1}.sort.bam && cp B17NC_R1.sort.bam.bai B17NC_R1${varible1}.sort.bam.bai
   done

8. Run the following commands to run the test case:

   cp /path/to/DELLY/delly-0.8.5/excludeTemplates/human.hg19.excl.tsv ./
   { time OMP_NUM_THREADS=128 delly call -x human.hg19.excl.tsv -o delly.bcf -g hg19.fa B17NC_R1*.sort.bam; }  2>&1 | tee -a  kp920-7265.log

   

   Delly performs parallelization at the sample level. Therefore, OMP_NUM_THREADS must be equal to or less than the number of samples. In this example, there are 128 samples and OMP_NUM_THREADS is 128.

   If the information shown in Figure 1 is displayed, the running is successful.

   Figure 1 Running result
   
9. Run the following command to convert the running result into the VCF format and view the command output:

   bcftools view delly.bcf > delly.vcf && cat delly.vcf | more

   Figure shows the command output.

   Figure 2 Command output