GetPileupSummaries intervals-list with Targeted Sequencing?

Question

[Manuel Sokolov Ravasqueira]

Hi!

I am applying the GetPileUpSummaries, for somatic variant calling starting from targeted sequencing .fasta. I aligned the file with the GrCh38 reference. And currently I am at the GetPileUpSummariesStep.

  gatk --java-options -Xmx200G GetPileupSummaries \
    -I $RECBAM \
    -L ???? \
    -O $OUTPUT \
    -V $GERM # Germline reference --> small_exac_common_3.hg38.vcf.gz

For the -L argument i need an intervals.bed file. Given the fact that my fasta is targeted sequencing, which file should I use here?

Best Regards, Manuel

[Pierre Lindenbaum]

how about using the bed file of your targets....

[Manuel Sokolov Ravasqueira]

thanks for the suggestion. how can i obtain the bedfile of my targets (kit is proprietary - can I obtain bed from fasta? if yes how?)

[Pierre Lindenbaum]

kit is proprietary

I can't imagine you get a targeted sequencing without having a BED file....

[Manuel Sokolov Ravasqueira]

they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for bed file is not a suitable option in the current scenario.

[Pierre Lindenbaum]

Asking for bed file is not a suitable option in the current scenario.

???????

[Manuel Sokolov Ravasqueira]

SOLVED by using bedtools -> bamToBed tool.

bedtools bamtobed -i  $SORTED_BAM > intervals.bed