Running GATK4 in Non-Spark Mode

Procedure

Use PuTTY to log in to the server as the root user.
Run the following command to create an index for the FASTA file:
```
bwa index -a bwtsw human_g1k_v37.fasta
```

Run the following commands to compare the fastq file:

gatk CreateSequenceDictionary -R human_g1k_v37.fasta -O human_g1k_v37.dict
bwa mem -M -t 64 human_g1k_v37.fasta SRR742200_1.fastq SRR742200_2.fastq > SRR7.sam

Run the following command to re-sort the gene sequence:

gatk ReorderSam -I SRR7.sam -O SRR7_reorder.bam -R human_g1k_v37.fasta

Run the following command to sort gene sequences by coordinate in descending order:
```
gatk SortSam -I SRR7_reorder.bam -O SRR7_sorted.bam --SORT_ORDER coordinate
```

Run the following command to add a head for the gene sequence:

gatk AddOrReplaceReadGroups -I SRR7_sorted.bam -O SRR7_addhead.bam -LB lib1 -PL illumina -PU unit1 -SM 20

Run the following command to deduplicate the gene sequences:

gatk MarkDuplicates -I SRR7_addhead.bam -M test.metric -O SRR7_markdup.bam

Run the following command to perform the recalibration:

Re-sort the FASTA reference files to generate the fai file:
```
samtools faidx human_g1k_v37.fasta > human_g1k_v37.fai
```

Add an index to the vcf file:

gatk IndexFeatureFile -F dbsnp132_20101103.vcf
gatk BaseRecalibrator -I SRR7_markdup.bam --known-sites dbsnp132_20101103.vcf -O SRR7_bqsr.bam -R human_g1k_v37.fasta
gatk ApplyBQSR -bqsr SRR7_bqsr.bam -I SRR7_markdup.bam -O SRR7_aybqsr.bam

Run the following command to check the HaplortypeCaller variation process:

gatk HaplotypeCaller -I SRR7_aybqsr.bam -O SRR7_raw.vcf -R human_g1k_v37.fasta

Parent topic: Running and Verifying GATK