Pindel user manual

Kai Yek.ye@lumc.nl

Preparation of Pindel inputAlignment BAM file generated by BWA

Alignment BAM file generated by other aligners

Pindel input with sample tag

(1) bam2pindel.pl Adaptor.pm

(2) sam2pindel.cpp

Filtered Pindel input with sample tag

(3) FilterPindelReads.cpp

Merge Pindel input files for paired or population sequence data

(1) bam2pindel.pl• Written by Keiran Raine at Sanger Institute (kr2@sanger.ac.uk)• This tool was designed for BWA based BAM/SAM Illumina data• You must prepare a name sorted bam file• Set BAM_2_PINDEL_ADAPT

setenv BAM_2_PINDEL_ADAPT <path to Adaptor.pm>• Arguments:

-i|input: Input BAM file (req)-o|output: Output ready for pindel-s|sample: Sample or label (sampA,sampB...) (req)-pi|insert: Required if BAM file does not have PI tag in header RG record-r|restrict: Restrict to chromosome xx

• Example: ./bam2pindel_bwa.pl –i NameSorted.bam –o output_prefix -s tumour –om –pi 300

(2) sam2pindel.cpp• Written by Kai Ye at Leiden University Medical Center (k.ye@lumc.nl)• This tool was designed for all BAM/SAM Illumina data• You must first compile the cpp source code: g++ sam2pindel.cpp –o sam2pindel –O3

• 5 arguments are required by sam2pindel– 1. Input sam file.– 2. Output for pindel.– 3. insert size.– 4. tag.– 5. number of extra lines (not start with @) in the beginning of the file.

• If you start with standard sam file (Input.sam with insert size 300) ./sam2pindel Input.sam Output4Pindel.txt 300 tumour 0• If you start with bam file ./samtools view Input.bam | ./sam2pindel - Output4Pindel.txt 300 tumour 0

Running Pindel1. Input: the reference genome sequences in fasta format;2. Input: the unmapped reads in a modified fastq format;3. Output folder4. Which chr/fragment5. BreakDancer result: Format per line: ChrA LocA stringA ChrB LocB stringB others If you don't have BreakDancer result, please provide an empty

file here.

Example:./pindel hg19.fa pindel_input_chr1.txt Output_Folder chr1 empty

Input format of Pindel

@9113TGGGGACCGGTGGAATGCTTCCACTGGCTGGGGGGC + chr2 41149518 50 Tumor

ref

Anchor

Strand, chr, 3’ coordinate and mapping quality of the mapped reads; sample tag

18 April 2023 7

Output format: deletions

1base - 1million bases

Allow mismatches to accommodate sequence errors and SNPs

D 10 ChrID 13 BP 32913041 32913052

AAATCAACTAGTGACCTTCCAGGGACAACCCGAACGTGATGAAAAGATCAaagaacctacTCTATTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGACAAAGT

GATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGACAA

CAACCCGAACGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGA

CGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGA

CGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGA

TGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGACAAAG

GTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGAC

TAGTGACCTTCCAGGGACAACCCGAACGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAA

CCTTCCAGGGACAACCCGAACGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAA

ACAACCCGAACGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGG

CGAACGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTT

CCCGAACGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATC

AACCCGAACGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAA

TGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGACA

ACCTTCCAGGGACAACCCGAACGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAA

GATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGACAA

AACCCGAACGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAA

GAACGTGATGAAAAGATCA TCTGTTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTT

8

Inversions

9

sample

ref

Large insertions

10

Non-template sequence in deletions, inversions and tandem duplications

11

ref

sample

Non-template sequence: deletion of 4 bases with 2 bases inserted

D 4 I 2 ChrID 3 BP 156978978 156978983 Supports 12 + 0 - 12 S1 13 SUM_MS 627 NumSupSamples 1 HCC1599a 12

CATGGCTGACTTATAAATCCCTACAGATATGTGGTTACTTCTCTACTTTCCCTTTCTTTGGCTTGGGCAACTGCCACGTTGATGCACTGGAGCCATTCTTCTGCATTCTTCTCATCCTTGGCCTTAAAGACATAGGTTTTATTGTC

TTATAAATCCCTACAGATATGTGGTTACTTCTCTACTTTCCCTTTCTTTGCCTTGGGCAACTGCCAAA GATGCACT

ATGTGGTTACTTCTCTACTTTCCCTTTCTTTGGCTTGGGCAACTGCCAAA GATGCACTGGAGCCATTCTTCTGCAT

CTCTACTTTCCCTTTCTTTGGCTTGGGCAACTGCCAAA GATGCACTGGAGCCATTCTTCTGCATTCTTCTCATCCT

AGATATGTGGTTACTTCTCTACTTTCCCTTTCTTTGGCTTGGGCAACTGCCAAA GATGCACTGGAGCCATTCTTCT

TTTCCCTTTCTTTGGCTTGGGCAACTGCCAAA GATGCACTGGAGCCATTCTTCTGCATTCTTCTCATCCTTGGCCT

TTCCCTTTCTTTGGCTTGGGCAACTGCCAAA GATGCACTGGAGCCATTCTTCTGCATTCTTCTCATCCTTGGCCTT

TTACTTCTCTACTTTCCCTTTCTTTGGCTTGGGCAACTGCCAAA GATGCACTGGAGCCATTCTTCTGCATTCTTCT

CTTGGGCAACTGCCAAA GATGCACTGGAGCCATTCTTCTGCATTCTTCTCATCCTTGGCCTTAAAGACATAGGTTT

CTACAGATATGTGGTTACTTCTCTACTTTCCCTTTCTTTGGCTTGGGCAACTGCCAAA GATGCACTGGAGCCATTC

AAATCCCTACAGATATGTGGTTACTTCTCTACTTTCCCTTTCTTTGGCTTGGGCAACTGCCAAA GATGCACTGGAG

CTTGGGCAACTGCCAAA GATGCACTGGAGCCATTCTTCTGCATTCTTCTCATCCTTGGCCTTAAAGACATAGGTTT

TTCCCTTTCTTTGGCTTGGGCAACTGCCAAA GATGCACTGGAGCCATTCTTCTGCATTCTTCTCATCCTTGGCCTT