Hi,I'm using GATK and samtools to call SNP.
For GATK:
java -Xmx6g -jar GenomeAnalysisTK.jar -R example.fa -T UnifiedGenotper -I sampleSort.bam -o GATK.vcf -mbq 30 -glm BOTH
For samtools:
samtools mpileup -Q 13 -ugf example.fa sampleSort.bam | bcftools view -bvcg > sample.raw.bcf
bcftools view sample.raw.bcf | vcfutils.pl varFilter -d 10 -w 5 -D 100 > samtools.vcf
But I find there is less common SNP between GATK.vcf and samtools.vcf, about 50% or less.
I don't know why ? Even though I have used a lot default value or other parameter , but the result between GATK and samtools is still out of my expectation.
How should I improve the concordance between GATK and Samtools ?
What's about your command or what should I pay attention to?
Thanks for your answer.
sunbert
For GATK:
java -Xmx6g -jar GenomeAnalysisTK.jar -R example.fa -T UnifiedGenotper -I sampleSort.bam -o GATK.vcf -mbq 30 -glm BOTH
For samtools:
samtools mpileup -Q 13 -ugf example.fa sampleSort.bam | bcftools view -bvcg > sample.raw.bcf
bcftools view sample.raw.bcf | vcfutils.pl varFilter -d 10 -w 5 -D 100 > samtools.vcf
But I find there is less common SNP between GATK.vcf and samtools.vcf, about 50% or less.
I don't know why ? Even though I have used a lot default value or other parameter , but the result between GATK and samtools is still out of my expectation.
How should I improve the concordance between GATK and Samtools ?
What's about your command or what should I pay attention to?
Thanks for your answer.
sunbert
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