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(How to) generate a complete realigned bam file using -bamout argument in HaplotypeCaller?
Hello, I want to get a realigned bam file for other tools to call variants, so I used the -bamout argument in HaplotypeCaller. I found that bam file is incomplete when I used only -bamout argument. When I set --disable-optimizations and -bamout arguments and added -forceActive and -dontTrimActiveRegions flags, error messages said that " A USER ERROR has occurred: f is not a recognized option". Maybe the program didn't recognize these flags. My command line is shown below:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /software/bin/gatk-package-18.104.22.168-local.jar HaplotypeCaller -R /root/data/reference/gatk_bundle/Homo_sapiens_assembly38.fasta -I /root/data/output/6_BQSR/SRR2188163.bqsr.bam --dbsnp /root/data/reference/gatk_bundle/dbsnp_146.hg38.vcf.gz -O SRR2188163.raw.2.vcf -bamout SRR2188163.bamout.2.bam --disable-optimizations true -forceActive -dontTrimActiveRegions
Could you tell me how I can use HplotypeCaller to get a complet realigned bam file? Thanks a lot.
The first picture is the screenshot of the output bam file which I used -bamout to generate. I used -bamout and --disable-optimizations arguments without add any flags to get the result in second picture. And I failed to add flags.