Snp Calling Error By Gatk Unifiedgenotyper Program

Question

[Tonyzeng]

HI, I have tried to do SNP calling using the GATK UnifiedGenotyper program,here is the command, (mouse)

java -jar /raid1/rzeng/softwares/GenomeAnalysisTK-2.7-4-g6f46d11/GenomeAnalysisTK.jar -glm BOTH -R genome.fa -T UnifiedGenotyper -I output.bam --dbsnp SNPMOUSENEW.vcf -o snps.vcf -metrics snps.metrics -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 200 -A DepthOfCoverage -A AlleleBalance -L targets.interval_list

Error message like this,

ERROR MESSAGE: Badly formed genome loc: Contig 'chr1    134202950    134203590    NM_001008533_cds_0_0_chr1_134202951_r    0    -' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?

Here is my targets.interval_list looks like,

chr1    134202950    134203590    NM_001008533_cds_0_0_chr1_134202951_r    0    -
chr1    134234014    134234355    NM_001008533_cds_1_0_chr1_134234015_r    0    -
chr1    134202950    134203590    NM_001039510_cds_0_0_chr1_134202951_r    0    -
chr1    134234014    134234355    NM_001039510_cds_1_0_chr1_134234015_r    0    -
chr1    134202950    134203590    NM_001282945_cds_0_0_chr1_134202951_r    0    -
chr1    134234014    134234355    NM_001282945_cds_1_0_chr1_134234015_r    0    -
chr1    25068167            25068356            NM_175642_cds_0_0_chr1_25068168_r            0    -
chr1    25074684       25074789            NM_175642_cds_1_0_chr1_25074685_r            0    -

I downloaded targets.interval_list from

http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=351729785&clade=mammal&org=Mouse&db=mm10&hgta_group=allTracks&hgta_track=refGene&hgta_table=0&hgta_regionType=genome&position=chr12%3A56694976-56714605&hgta_outputType=bed&hgta_outFileName=targets.interval_list

Anyone can help me take a look at it....?

Thank you,

Answer 1

[Pierre Lindenbaum]

try to use

-L:capture,BED targets.interval_list

instead of

-L targets.interval_list

also check that the chromosome names are the same as in the reference, and check that you did not change the 'tab's to spaces.

Answer 2

[vdauwera]

My bet is that the tabs got changed to spaces, which is why the program is reading the entire line in as the contig.

Answer 3

[Tonyzeng]

HI guys, I have changed and shortened commands as follows for making it simple, it works this time,Thank you,

java -jar /raid1/rzeng/softwares/GenomeAnalysisTK-2.7-4-g6f46d11/GenomeAnalysisTK.jar -glm BOTH -R genome.fa -T UnifiedGenotyper -I output.bam --dbsnp SNPMOUSENEW.vcf -o snps.vcf -metrics snps.metrics -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 200