merge

sed -i 's/YING\../YING/g' 7550x1.merged.sam

sed -i 's/novoalign\../novoalign/g' 7550x1.merged.sam

time java -jar -Xmx30g ~/tool/picard-tools-1.41/SortSam.jar INPUT=7550x1.merged.sam OUTPUT=7550X1.merged.bam CREATE_INDEX=true SO=coordinate COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=7500000 TMP_DIR=.

time java -jar -Xmx30g ~/tool/gatk/dist/GenomeAnalysisTK.jar -T UnifiedGenotyper -R chr20.fa -B:dbsnp,VCF dbsnp132.human.vcf -o 7550X1.snps.raw.vcf -I 7550X1.merged.bam -stand_call_conf 50.0 -stand_emit_conf 20.0 -dcov 300

time java -jar -Xmx32g ~/tool/gatk/dist/GenomeAnalysisTK.jar -T VariantFiltration -R chr20.fa -B:variant,VCF 7550X1.snps.raw.moab.vcf -o 7550X1.snps.raw.moab.homosnp.vcf --maskName InDel --clusterWindowSize 10 --filterExpression "AF<1.0 || DP<10 || DP>100" --filterName "AF<1.0 or DP<10"

grep -c "PASS" 7550X1.snps.raw.moab.homosnp.vcf