FLT3_ITD_Pindel

detect FLT3-internal tandem duplication using Pindel

Usage

perl /path/FLT3_ITD_Pindel/TandemDupScan.pl -bam <bam file> -n <name> -flen <fragment length> -fa <fasta> -pindel <path to binary pindel> -od <outdir>

paramerter specification

-bam: bam file

-n: sample name

-flen: DNA fragment length. default: 500

-fa: fasta file

-pindel: binary pindel

-od: output dir

Testing

1. cd /path/FLT3_ITD_Pindel/test/res
2. sh run.sh
3. sh test.pindel.sh >log 2>&1 &

result files

-rw-r--r--  1 lffu  staff    24K  9 18 14:55 log
-rw-r--r--  1 lffu  staff    85B  9 18 14:55 pinde.cfg
-rw-r--r--  1 lffu  staff    66B  9 18 14:55 run.sh
-rw-r--r--  1 lffu  staff   1.1K  9 18 14:55 test.ins.vcf
-rw-r--r--  1 lffu  staff   1.0K  9 18 14:55 test.pindel.sh
-rw-r--r--  1 lffu  staff   1.7K  9 18 14:55 test.td.final.vcf
-rw-r--r--  1 lffu  staff   1.8K  9 18 14:55 test.td.vcf
-rw-r--r--  1 lffu  staff     0B  9 18 14:55 test_BP
-rw-r--r--  1 lffu  staff     0B  9 18 14:55 test_CloseEndMapped
-rw-r--r--  1 lffu  staff     0B  9 18 14:55 test_D
-rw-r--r--  1 lffu  staff     0B  9 18 14:55 test_INT_final
-rw-r--r--  1 lffu  staff   3.8K  9 18 14:55 test_INV
-rw-r--r--  1 lffu  staff     0B  9 18 14:55 test_LI
-rw-r--r--  1 lffu  staff     0B  9 18 14:55 test_RP
-rw-r--r--  1 lffu  staff     0B  9 18 14:55 test_SI
-rw-r--r--  1 lffu  staff    76K  9 18 14:55 test_TD

Note

• short tandem dup will be stored in _SI file

• long tandem dup will be stored in _TD file

*.ins.vcf: short tandem dup vcf file

*.td.vcf: long tandem dup vcf file

*.td.final.vcf: final tandem dup vcf file

filter process

for _SI file

1. HOMLEN > 0
2. ref POS column need to be included by the positions of alt seq
3. alt num >= 2
4. SVLEN >= 2

step2 details

#1. get ins seq from ALT column in *.ins.vcf

#2. find all positions of ins seq in ref (allow one mismatch)

#3. check if POS column in *.ins.vcf is included by the finded postions in #2

#4. if the POS column is included, then this variant will output in the final result file *.td.final.vcf

for _TD file

1. no filter

about Pindel

install

conda install -c bioconda pindel

origin paper

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads, Bioinfomatics, 2009

source code

https://www.sanger.ac.uk/tool/pindel/

https://github.com/genome/pindel