Key SOMATIC in field INFO is not defined in the VCF file header for of indel calls

[csb5]

Key SOMATIC in field INFO is not defined in the VCF file header for of indel calls

[andreas-wilm]

Hey Hongen, sorry about this.

You can fix existing files by adding the following line to the vcf header: ##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic event">

Commit 7086354 fixed the issue.

Thanks for reporting,
Andreas

[NitinMandloi]

lofreq call-parallel --pp-threads 8 --call-indels -l file.bed --ref hg19.fa -o out.vcf input.bam

WARNING [2016-10-24 13:24:13,952]: Regions getting too small to be efficiently processed
INFO [2016-10-24 13:24:13,963]: Adding 19 commands to mp-pool
Number of substitution tests performed: 4476
Number of indel tests performed: 285
INFO [2016-10-24 13:24:28,884]: Executing lofreq filter -i /tmp/lofreq2_call_parallelbAdZ7k/concat.vcf.gz -o 30277_10000x_7985.vcf --snvqual-thresh 57 --indelqual-thresh 45

Why lofreq is not reporting any indel for me.

[NitinMandloi]

Any specific format for BAM file required

[andreas-wilm]

Did pre-process the BAM file with GATK's BSQR or lofreq indelqual so that indel qualities were inserted?

[NitinMandloi]

I just align the reads with BWA-MEM and sam to bam conversion and sorting with samtools.

[NitinMandloi]

Got it. I need to use --dindel option.

Thank you

Regards

[andreas-wilm]

This won't work. You need GATK's BQSR or lofreq indelqual as mentioned in
the documentation

On 24 October 2016 at 17:00, NitinMandloi [email protected] wrote:

I just align the reads with BWA-MEM and sam to bam conversion and sorting
with samtools.

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