gatk变异检测

使用GATK完成变异检测。但在开始之前之前我们还需要先为参考序列生成一个.dict文件，这可以通过调用CreateSequenceDictonary模块来完成(这是原来picard的功能)。

/public/home/fengting/tools/gatk-4.1.7.0/gatk CreateSequenceDictionary \
-R ~/database/rice/ribenqing/IRGSP-1.0_genome.fasta \
-O ~/database/rice/ribenqing/IRGSP-1.0_genome.dict

markdup

cat  id |while read id 
do
echo "~/tools/gatk-4.1.7.0/gatk MarkDuplicates --INPUT bams/$id.bam --OUTPUT mkbam/${id}.bam --METRICS_FILE mkbam/${id}.bam.txt --VALIDATION_STRINGENCY SILENT --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --ASSUME_SORT_ORDER "coordinate" --CREATE_INDEX true" >>mak.sh

done

##~/tools/gatk-4.1.7.0/gatk MarkDuplicates --INPUT bams/DC001-1_C001.bam --OUTPUT mkbam/DC001-1_C001.bam --METRICS_FILE mkbam/DC001-1_C001.bam.txt --VALIDATION_STRINGENCY SILENT --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --ASSUME_SORT_ORDER coordinate --CREATE_INDEX true

picard添加GROUP

cat id|while read id
do

echo "picard AddOrReplaceReadGroups -I bams/$id.bam -O group/$id.bam --RGID sample1 --RGLB lib1     --RGPL illumina     --RGPU unit1     --RGSM sample1     --VALIDATION_STRINGENCY LENIENT     -Xms1g -Xmx10g -XX:ParallelGCThreads=10" >>gr.sh
done
#picard AddOrReplaceReadGroups -I bams/DC001-1_C001.bam -O DC001-1_C001.bam --RGID sample1 --RGLB lib1     --RGPL illumina     --RGPU unit1     --RGSM sample1     --VALIDATION_STRINGENCY LENIENT     -Xms1g -Xmx10g -XX:ParallelGCThreads=10

call

cat id|while read id
do
echo "~/tools/gatk-4.1.7.0/gatk HaplotypeCaller -R ~/database/rice/ribenqing/IRGSP-1.0_genome.fasta -I bams/$id.bam -O gvcf/$id.g.vcf -ERC GVCF" >>gk.sh
done

.GVCF文件合并

gatk --java-options "-Xmx100g -XX:ParallelGCThreads=4" CombineGVCFs \
    -R ~/ref/Mparg_v2.0.fa \
    -V LPF1_R1_MP.g.vcf.gz \
    -V LPF1_R2_MP.g.vcf.gz \
    -V LPF1_R3_MP.g.vcf.gz \
    -O LPF1_MP.g.vcf.gz

参考：
Blaming Rice_Heterosis/variant_calling_pipeline/variant_calling_pipeline.txt at main · zlguu/Rice_Heterosis · GitHub

[picard——修改BAM文件的Read Group - 简书 (jianshu.com)]
(https://www.jianshu.com/p/de1c027e672b)

GATK4 —— 获取短变异 （call SNP+indel） - 简书 (jianshu.com)