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How can I find Variants position by GATK and Samtools

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

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

snp samtools gatk
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updated by Biostar Biostar • written by Mbillah Mbillah

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...

• 1 views • link
written by WouterDeCoster WouterDeCoster

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

• 1 views • link
written by Mbillah 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

• 1 views • link
written by Mbillah Mbillah

No, It's haploid goat

• 1 views • link
written by Mbillah Mbillah

Hello,

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

fin swimmer

• 1 views • link
written by finswimmer finswimmer

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