-I sample1.bam [-I sample2.bam ...] \ [--dbsnp dbSNP.vcf] \ [-stand_call_conf 30] \ [-L targets.interval_list] \ -o output.raw.snps.indels.vcf RNA-seq variant-calling java -jar GenomeAnalysisTK.jar \ -R reference.fasta \ -T HaplotypeCaller \ -I sample1.bam \ [--dbsnp ...
bam --dbsnp /public/home/$db_snp.vcf --native-pair-hmm-threads 8 -stand-call-conf 30 -L XXXX.intervals -O XXX.2.g.vcf.gz -ERC GVCF XXXX.intervals的内容格式,根据你的gtf注释文件决定,如果是chr1格式,则文件里面应该是chrn,如果和我的一样,直接是1这种方式表示染色体号,则如下所示即可。一...
In addition, comparative studies usually measure the accuracy with summary statistics such as the fraction of calls present in dbSNP or the transition-to-transversion ratio. They do not tell us the wrong sites’6. Indeed, obtaining correct SNVs positions across the whole genome is almost ...
GPU options: --num-gpus NUM_GPUS Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used. Note In the values provided to--haplotypecaller-options--output-mode requires two leading hyphens, while all other values take a single hyphen. ...