Dear All,
I have a bam file aligned to a reference genome. I would like to know if there is a way to calculate the over all length of aligned genome.
Thanks in advance. Sam.
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sambioinfo2018 •
genomecov should do what you are asking for
Edit :
May take a while :
output=$(bedtools genomecov -ibam in_file.bam -d -split) && (echo "scale=2; $(echo "$output" | cut -f3 | grep -vc "0")/$(echo "$output" | wc -l)" | bc)
Thanks Bastien. Is this the command to do so:
bedtools genomecov -ibam bamfile.bam -bga -g genomelength.txt
More something like this (get the depth at each position):
bedtools genomecov -ibam input_file.bam -d -split > output_depth.txt
From the output file (output_depth.txt), count the number of line with NOT 0 in the 3rd column (with awk for example) divided by the number of line in the file. You will get the percentage of reference positions covered by at least one read.
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