SNP calling

biobaby

为什么用HaplotypeCaller  算法call SNP 时， call 到的结构第三列没有rs号信息。 而且 之后的矫正过程中并不能把SNP和 indel分开。
下面是我的代码：
java -Xmx4g -jar /leofs/yangyg_group/zhaoxu/shy/SNP/soft/GenomeAnalysisTK/GenomeAnalysisTK.jar -T HaplotypeCaller -stand_call_conf 30 -stand_emit_conf 10 -R /leofs/yangyg_group/zhaoxu/hg19/gatk/hg19.fa -I all.dup.realig.recal.bam -D /leofs/yangyg_group/zhaoxu/sunbf/0gatk/dbsnp_138.hg19.vcf  -o all_snp.vcf


#########Variant quality score recalibration

java -Xmx4g -jar /leofs/yangyg_group/zhaoxu/shy/SNP/soft/GenomeAnalysisTK/GenomeAnalysisTK.jar -T VariantRecalibrator -R /leofs/yangyg_group/zhaoxu/hg19/gatk/hg19.fa -mode SNP -input all_snp.vcf -resource:hapmap,known=false,training=true,truth=true,prior=4.0 /leofs/yangyg_group/zhaoxu/sunbf/0gatk/hapmap_3.3.hg19.vcf -resourcemni,known=false,training=true,truth=true,prior=12.0 /leofs/yangyg_group/zhaoxu/sunbf/0gatk/1000G_omni2.5.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /leofs/yangyg_group/zhaoxu/sunbf/0gatk/1000G_phase1.snps.high_confidence.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /leofs/yangyg_group/zhaoxu/sunbf/0gatk/dbsnp_138.hg19.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -recalFile all_snp.recal -tranchesFile all_snp.tranches -rscriptFile all_snp.plots.R


java -Xmx4g -jar /leofs/yangyg_group/zhaoxu/shy/SNP/soft/GenomeAnalysisTK/GenomeAnalysisTK.jar -T VariantRecalibrator -R /leofs/yangyg_group/zhaoxu/hg19/gatk/hg19.fa -mode INDEL -input all_snp.vcf -resource:mills,known=false,training=true,truth=true,prior=12.0 /leofs/yangyg_group/zhaoxu/sunbf/0gatk/Mills_and_1000G_gold_standard.indels.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /leofs/yangyg_group/zhaoxu/sunbf/0gatk/dbsnp_138.hg19.vcf -an QD -an FS -an ReadPosRankSum -an MQRankSum -recalFile all_indel.recal -tranchesFile all_indel.tranches -rscriptFile all_indel.plots.R --maxGaussians 4 --percentBadVariants 0.05

Herowinter

不明觉厉

zhleiling

目测楼主进错区了