Question: Somatic indel calling with Pindel
gravatar for sichan
4.1 years ago by
sichan80 wrote:


I noticed that Pindel was previously reported to not be able to call somatic indels without post-processing, e.g. see these posts:
Pindel Somatic Calls?

However, I noticed that the latest version of Pindel (0.2.5b1) has the --NormalSamples option.  According to the usage prompt, this flag turns on germline variant filtering:

Turn on germline filtering, less sensistive and you may miss somatic calls (default false)

I run Pindel as follows:
pindel -f hg19.fa -i bam_config_file.txt -o Test1 --NormalSamples

My bam configuration file looks like:
/path/to/tumor/bam  insert_size Tumor
/path/to/normal/bam insert_size Normal

However, I noticed that the output still contains germline indels.  So perhaps the --NormalSamples hasn't been fully implemented yet and I'll still need to post-process results to get somatic indels from Pindel?

Thanks for any suggestions.

somatic pindel indels • 2.0k views
ADD COMMENTlink modified 10 weeks ago by Kevin Blighe46k • written 4.1 years ago by sichan80
gravatar for Kevin Blighe
10 weeks ago by
Kevin Blighe46k
Kevin Blighe46k wrote:

A late answer but I am currently using Pindel.

Current versions (now June 8th, 2019) do perform somatic indel calling.

Here is my config file:

BB40.bam        150 Tumor
BM_Control.bam  150 Normal

Here are my commands to loop through each chromosome (mouse; excluding sex chromosomes):

mkdir pindel/ ;

for chr in {1..19}; do
  mkdir pindel/chr"${chr}"/

  /Programs/pindel/pindel \
    --fasta /ReferenceMaterial/mm10/mm10.fasta \
    --config-file pindelConfigs/BM39.txt \
    --chromosome chr"${chr}" \
    --number_of_threads 2 \
    --min_num_matched_bases 30 \
    --report_inversions TRUE \
    --min_inversion_size 50 \
    --report_duplications TRUE \
    --report_long_insertions TRUE \
    --report_breakpoints TRUE \
    -o pindel/chr"${chr}"/ ;

  /Programs/pindel/pindel2vcf \
    --pindel_output_root pindel/chr"${chr}"/ \
    --reference /ReferenceMaterial/mm10/mm10.fasta \
    --reference_name mm10 \
    --reference_date 99999999 \
    --min_coverage 1 \
    --het_cutoff 0.01 \
    --hom_cutoff 0.99 \
    --vcf pindel/chr"${chr}"/chr"${chr}".vcf ;

  bgzip -f pindel/chr"${chr}"/chr"${chr}".vcf ;

  tabix -f -p vcf pindel/chr"${chr}"/chr"${chr}".vcf.gz ;

  /Programs/bcftools-1.9/bcftools view -Ov --exclude-uncalled --min-ac=1 pindel/chr"${chr}"/chr"${chr}".vcf.gz > pindel/chr"${chr}"/chr"${chr}".filt.vcf ;

The resulting VCFs contain the calls for the tumor and normal sample, and indicate presence or absence in both.


ADD COMMENTlink written 10 weeks ago by Kevin Blighe46k

thanks for this, exactly what I was looking for

ADD REPLYlink written 7 weeks ago by steve2.2k
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