<jupyter_start><jupyter_text>generate statistical data of gatk & vardict> tools: >> gatk VariantEval>> picard CollectVariantCallingMetrics some bugs with vardict vcf, may be compartibility reason<jupyter_code>%%bash 

picard -Xmx2048m CollectVariantCallingMetrics \
I=/mnt/data_sata_2t/vsftpd/wxq/ftp/files/0306/HY19020837.vardict.vcf.gz \
O=/mnt/data_sata_2t/vsftpd/wxq/ftp/files/0306/HY19020837.vardict.metrics \
DBSNP=/home/jgs/database/gatk_bundle/GRCh37/ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf \
TI=/mnt/data_sata_2t/vsftpd/wxq/ftp/files/0306/target.interval_list

picard -Xmx2048m CollectVariantCallingMetrics \
I=/mnt/data_sata_2t/vsftpd/wxq/ftp/files/0306/HY19020837.vcf.gz \
O=/mnt/data_sata_2t/vsftpd/wxq/ftp/files/0306/HY19020837.gatk.metrics \
DBSNP=/home/jgs/database/gatk_bundle/GRCh37/ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf \
TI=/mnt/data_sata_2t/vsftpd/wxq/ftp/files/0306/target.interval_list
%%bash

gatk VariantEval \
--eval HY19020837.vcf.gz \
--eval HY19020837.vcf.gz \
-R ~/database/gatk_bundle/b37/human_g1k_v37.fasta \
-O ./compare.tab<jupyter_output><empty_output>
StarcoderdataJupyterStructuredCleanDedup