Question about the concordance between GATK and Samtools

[sunbert]

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

[vdauwera]

I recommend you show the details of your analysis. Say what data you analyzed, how you did it, what are the results, and why you think the results are problematic. If you do not give this information, nobody can help you.

[swbarnes2]

At first guess, I'd try doing a much more stringent quality filter, and you might get more concordance. My guess is that a lot of the discrepancies are stupid false positives.

[sunbert]

I recommend you show the details of your analysis. Say what data you analyzed, how you did it, what are the results, and why you think the results are problematic. If you do not give this information, nobody can help you.

okay,thanks for your advise 。
I hava a sam formate file which is from bowtie alignment after sequencing(whole genome sequence ).
I would like to know the SNPs in this data for next analysis.
First, I convert the sam file to bam file. Second, I use samtools to sort the bam file. Then I use samtools and GATK to call SNP.
But I find the proportion of common SNP is too low ,about 50% or less. That's to say some SNPs GATK can call out but samtools can't, and some SNPs samtools can call out but GATK can't. That's so strange!
There must be wrong somewhere.

[sunbert]

At first guess, I'd try doing a much more stringent quality filter, and you might get more concordance. My guess is that a lot of the discrepancies are stupid false positives.

Yeah, I agree with you .
I think there have lots of false positives in the result.
More stringent quality filter dosen't seem to work for I have tried . I may be forget other parameter or step.But I can't find where to correct, my command seem normal with others.