Hello Everyone,

I am trying to do read depth calling of chromosomes from bam files of the exome sequencing data. I am still in the early stages of learning bioinformatics. Initially I thought of doing read depth calling for chromosomes 1 through 22 only. I used the following code. I split the job into different individual arrays using the option "-t 1-22". This option doesn't allow me to include the X-chromosome in it.

!/bin/bash

$ -q long

$ -t 1-22

$ -cwd

$ -j y

$ -l m_mem_free=32g

source /software/scripts/useuse reuse -q Tabix reuse -q Samtools

samtools mpileup -ABQ0 -d 250 -b finnish.sample.list -f cvar/reddy/human_g1k_v37.fasta -l /cvar/reddy/RefSeq_bed/RefSeq_exons_trim_chr${SGE_TASK_ID}.bed -t DP -uv > finnish_rdepths.chr$SGE_TASK_ID.vcf

Then now I want to include X chromosome for read depth calling. I tried to change this code like this. 1) I removed the option "-t 1-22" and launched the same job using qsub. This produced an error - "/cvar/reddy/RefSeq_bed/RefSeq_exons_trim_chrundefined.bed": No such file or directory. 2) I changed the code as follows - since I need the read depths of only X-chromsomes (other chromosomes already done) samtools mpileup -ABQ0 -d 250 -b finnish.sample.list -f cvar/reddy/human_g1k_v37.fasta -l /cvar/reddy/RefSeq_bed/RefSeq_exons_trim_chrX.bed -t DP -uv > finnish_rdepths.chrX.vcf

This produced an output file with all the headers and individual IDs and no data in it.

I am not sure where I am doing anything wrong and would appreciate any suggestions or modification regarding the code I am using to perform read depth calling either for X chromosome alone or 1-22 & X chromosome combined.