Produce raw SNP calls

Question

[cristina_sabiers]

I will dance around my pc if get this last step XD

I try call my snps with this code

java -Xmx4g -jar /home/cri/Desktop/GATK/GenomeAnalysisTK.jar \
-glm BOTH \
-R hg19.fa \
-T UnifiedGenotyper \
-I input.header.realigned.bam \
-D dbsnp138.txt \
-o snps.vcf \
-metrics snps.metrics \
-stand_call_conf 50.0 \
-stand_emit_conf 10.0 \
-dcov 1000 \
-A DepthOfCoverage \
-A AlleleBalance \
-L target_intervals.bed

but I get this error message

ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file 'dbsnp138.txt' could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR Name      FeatureType   Documentation
##### ERROR BCF2   VariantContext   (this is an external codec and is not documented within GATK)
##### ERROR  VCF   VariantContext   (this is an external codec and is not documented within GATK)
##### ERROR VCF3   VariantContext   (this is an external codec and is not documented within GATK)

I downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/snp138.txt.gz

Someone knows why I get this error?

Thanks

[cristina_sabiers]

well meanwhile I waited for down my vcf.gz fle for gatk I tried another code with freebayes

bin/freebayes --min-coverage 10 -V -f /media/cri/CRIS_DATA/ULT/OTRO2/otro/hg19.fa /media/cri/CRIS_DATA/ULT/OTRO2/otro/input.header.realigned.bam >/media/cri/CRIS_DATA/ULT/OTRO2/otro/freebayessample.vcf

FINALLY I GOT MY SNPS AND INDELS!!!! ALELUYAAAAAAAAAAAAAAA

[GenoMax]

Did you dance around your PC as promised :-D

[cristina_sabiers]

hahahha yes I did!!! XDDDD

Thanks to all for the help!

Now comes the most interesting part...work with vcf file

Answer 1

[William]

The dbsnp138 file does not seem to be recognized as valid type of file that GAKT can handle , and it probably also does not have an index.

You could try to use the DBSNP file (plus index file) that is provided by GATK in the resource bundle. http://gatkforums.broadinstitute.org/gatk/discussion/1213/whats-in-the-resource-bundle-and-how-can-i-get-it

[cristina_sabiers]

thanks! I will try with File: Homo_sapiens_assembly38.dbsnp.vcf.gz hope is the right one :)