Thanks Chirag. Rectified the above error. Retried with
java -jar /../GenomeAnalysisTK-2.6-5-gba531bd/GenomeAnalysisTK.jar -R /data/../REF_GENOME_hg19/hg19_karyotypic.fa -T UnifiedGenotyper -I /data/../AD1cordsortrealigned.bam -o outprefix.snps.vcf -stand_call_conf 50.0 -stand_emit_conf 10.0
and now I'm getting:
##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
##### ERROR reads contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]
##### ERROR reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY]
I cannot see the option `-vf` in https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_genotyper_UnifiedGenotyper.php
You are right, Pierre. Ive removed that I believe it was for an old version now the default output is only vcf files. Now im getting an error saying "strictness is silent".
You are right, Pierre. Ive removed that I believe it was for an old version now the default output is only vcf files.
I retried with
Now I'm getting the error:
The GATK no longer supports SAM files without read groups.