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call variants for a single sample using HC

I am using HC and the following command to call variants for a single sample using the genotyping_mode DISCOVERY. This is still running.
java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R ${reference} \
-I ${result}/reduced_reads.bam \
-L chr21 \
--genotyping_mode DISCOVERY \
-stand_emit_conf 10 \
-stand_call_conf 30 \
-o ${result}/raw_variants.vcf

Came across another command in Best Practices document.
–T HaplotypeCaller\
–R human.fasta \
–I sample1.bam \
–o sample1.g.vcf \
-­‐-­‐variant_index_parameter 128000

Can you please let me know the difference and what command do I need to call variants for a single sample?
Output is a gvcf which is an intermediate step followed by VCF file.

Best Answers


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