How can I find Variants position by GATK and Samtools

Question

[Mbillah]

I am try to find out variants by GATK and Samtools. After generated vcf file by GATK and samtools I am trying to find out the variants difference by their position. But they could not find any match according to their position. That means GATK and Samtools variants position is not match. So what does GATK position means?

GATK:

#CHROM POS
NC_030808.1 38229
NC_030808.1 94732

NC_030808.1 94802

.................

.................

Samtools:

#CHROM POS

NC_030808.1 313
NC_030808.1 335
NC_030808.1 346
NC_030808.1 877
NC_030808.1 880
...............

...............

[WouterDeCoster]

Since both outputs are a vcf file, the position means the same: the position on the chromosome where the variant is found. It just seems that samtools calls variants way earlier (telomeric) than GATK. Perhaps you should scroll a little further in the samtools file...

[Mbillah]

This is the problem, their is no variants in position 38229, 94732,.... in samtools produced file.

[WouterDeCoster]

Please add the commands you used.

[Mbillah]

Samtools

samtools mpileup -g -f ref.fna out.sorted.bam > out.bcf

bcftools view -c -v out.bcf > out.vcf

GATK

java -jar /data/Softwares/GenomeAnalysisTK.jar -T HaplotypeCaller -R data/ref.fna -I realigned.bam -ploidy 1 -stand_call_conf 30 -stand_emit_conf 10 -o raw.vcf

[WouterDeCoster]

Do you have a monoploid goat?

[Mbillah]

No, It's haploid goat

[finswimmer]

Hello,

your samtools/bcftools commands looks like you are using a very old version. Upgrade to the latest first before further investigation.

fin swimmer

[Pierre Lindenbaum]

samtools mpileup (well it's should be 'bcftools mpileup' now) should be followed by bcftools call not bcftools view

see http://www.htslib.org/workflow/