The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

#### ☞ Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ` ) each to make a code block as demonstrated here.

Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the github release page for download and details.

# Can I force GATK UG to call SNP / Indel on a aligned bac contig (coverage of 1)?

Member

Can I force GATK UG to call SNP / Indel on a aligned bac contig (coverage of 1)? I tried to put -stand_call_conf and -stand_emit_conf on zero but I stil got a vcf file with just a header and no calls.

I have aligned a BAC contig with BWA mem to a reference sequence and I want to extract the SNP's and Indels that the BAC contig supports.

When I have those SNPs and InDels in a vcf file I can use them together with my SNP and INdels from NGS data to get the genotype concordance (with the genotype concordance tool. )

And I can use them for VQSR.

Tagged: