Picard tools samtofastq for a folder

Question

[Cindy]

I want to use SamToFastq in Picard tools to convert 100 bam files to fastq (pair-end). I wrote a loop, but it does not work. Anyone can help me to look at the code. I have no idea what's going on. Appreciate ahead.

#!/bin/bash
bamfolder="/path/to/folder/*"
for b in $bamfolder
do   
    echo $b   
    java -jar picard.jar SamToFastq \
    I=$b \
    FASTQ= /path/to/folder/*_R1.fastq \
    SECOND_END_FASTQ= /path/to/folder/*_R2.fastq
done

[GenoMax]

Are you getting anything back from echo $b. There can be no spaces between FASTQ= and SECOND_END_FASTQ= and the paths.

[Cindy]

When I run echo $b done, It listed all bam files in the folder.

[GenoMax]

This is academic since @Pierre's solution works but the reason yours is not working is because your are passing $b as the entire file name (with .bam extension intact). So instead if you try the following and see if that works.

for b in $bamfolder
do
    echo $b
    java -jar picard.jar SamToFastq \
    I=$b \
    FASTQ=/path/to/folder/${b%.*}_R1.fastq \
    SECOND_END_FASTQ=/path/to/folder/${b%.*}_R2.fastq
done

[Cindy]

I have tried. ERROE: Neither file nor parent directory exist.

I think for the "FASTQ=" and "SECOND_END_FASTQ=" I can not use /path/to/folder/${b%.*}, because it shows output=/path/to/folder/path/to/folder/. If only use FASTQ=${b%.bam}_R1.fq.gz, it works.

[GenoMax]

As is customary with these /path/to/folder/ is a placeholder that needs to be replaced with a real path available on your computer. It is there to show that you can use/write data from/to any other location.

[h.mon]

Does not work? How it doesn't work? What is the error message?

Anyway, I think there should not be spaces after FASTQ= and SECOND_END_FASTQ=.

[Cindy]

erroe msg is INPUT is required. It's kind wired. I think the I=$b is right....

Answer 1

[Pierre Lindenbaum]

find dir/ -name "*.bam" | while read F ; do  java -jar picard.jar SamToFastq I=$F FASTQ=${F%.bam}_R1.fq.gz SECOND_END_FASTQ=${F%.bam}_R2.fq.gz ; done

[Cindy]

Thanks. It works!!! Can I generate a folder call fastq under the "/path/to/folder/" to output all fastq using the same input filename?

[Pierre Lindenbaum]

it it works, please, check the green mark on the left to close the question.

Use 'mkdir -p ' to create a directory

[Cindy]

I appreciate your help!

Answer 2

[badribio]

#!/bin/bash
bamfolder="/path/to/folder/*"
for b in $bamfolder
do   
    echo ${b}
    java -jar picard.jar SamToFastq \
    I=$b \
    FASTQ=/path/to/folder/{b}_R1.fastq \
    SECOND_END_FASTQ=/path/to/folder/{b}_R2.fastq
done

space edited per @genomax2

[Cindy]

I have tried, same error: ERROR: Option 'INPUT' is required. I don't know why it's always request INPUT

Answer 3

[Cindy]

That's my final code and it works. First, use SamToFastq to generate *_R1_fq.gz and *_R2_fq.gz, then use mkdir and mv to move all fastq files to a new folder.

find /path/to/folder/ -name "*.bam" | while read F ; 
do   
    java -jar picard.jar SamToFastq \
         INPUT=$F \
         FASTQ=${F%.*}_R1.fq.gz \
         SECOND_END_FASTQ=${F%.*}_R2.fq.gz 
done

bamfolder="/path/to/folder/*.fq.gz"
for b in $bamfolder
do
fastq="/path/to/folder/fastq/"
mkdir -p $fastq
mv $b $fastq/
done