Indexed Ref File

[yikang7720]

Hi,

I am wondering what is the correct format of ref file. When I directly set the hg19.fa/hg38.fa as the ref file (python SeCNV.py dedup output hg19.fa/hg38.fa), it states an error said that "Could not find indexes". Then I used bwa index hg19.fa/hg38.fa, which generates a few files such as hg19.fa.amb, hg19.fa.ann files. I tried to set them as the ref file, it also does not work.

Can you please provide more information about the correct formats of ref file?

[wangruohan111]

Hi, yikang,

In which step it reports the error "Could not find indexes"? If the error occurs when you align FASTQ files to the reference genome for bioinformatic pre-processing, it means BWA does not successfully index the references. If the error occurs when you run python SeCNV.py, it means you did not index the bam files, please use "java -jar picard.jar BuildBamIndex I=file_name.sorted.rg.dedup.bam" as introduced in the readme file.

Ruohan

[yikang7720]

Hi Ruohan,

It reports the error at the last step, python SeCNV.py step. I used the "java -jar picard.jar BuildBamIndex I=file_name.sorted.rg.dedup.bam", and it gives a lot of bai files. I stored all the bai files into a folder but the SeCNV.py does not accept the reference folder.

Sincerely
Yikang

[wangruohan111]

Hi, Yikang,

It seems that the error is caused by counting reads with "bedtools multicov". Are the "*sorted.rg.dedup.bam" files and "*sorted.rg.dedup.bai" files all in the input directory？

Best regards,
Ruohan

[yikang7720]

Dear Ruohan,

They are all in the input directory. However, it states another error "processing chromosomes Could not open input BAM files." I googled it but i still cannot solve it. Can you please help me with it? Or maybe share your processed data with me?
Thank you so much for your help.

sincerely
Yikang