Bedtools multicov output file error

Question

[RK]

Hello,

I ran bedtools multicov for 5 bam files. The output file is corrupted after a certain set of time i.e, from chr13 to chrM the output generated as below :

tail multicov.txt output  - error

6500 chrX 140406100 140406600 chrX 140406200 140406700 chrX 140406300 140406800 chrX 140406400 140406900 chrX 140406500 140407000 chrX 140406600 140407100 chrX 140406700 140407200 chrX 140406800 140407300 chrX 140406900 140407400 chrX 140407000 140407500 chrX140407100 140407600 chrX 140407200 140407700 chrX 140407300 140407800 chrX 140407400 140407900 chrX 140407500 140408000 chrX 140407600 140408100 chrX 140407700 140408200 chrX 140407800 140408300 chrX 140407900 140408400 chrX 140408000

head multicov.txt output :
chr1    0   500 0   0   0   0   0
chr1    100 600 0   0   0   0   0
chr1    200 700 0   0   0   0   0
chr1    300 800 0   0   0   0   0
chr1    400 900 0   0   0   0   0

but the output is good for first 13 chromosomes. can anyone identify what could be the error possibly.

Thanks

[Nicolas Rosewick]

Could you edit your question to add the output ?

[RK]

added the output.

[Pierre Lindenbaum]

run samtools quickcheck on your bams

[RK]

samtools quickcheck *bam && echo 'all ok' \ || echo 'fail!'

all ok

• I guess the bam files are not truncated as quickcheck didnot show any failed files.

Answer 1

[RK]

Is it possible that the unequal number of fields across the bam file is affecting the multicov output? Like some reads have 16 fields, some have 12 etc. The bam file follows the samtools format and has the first 11 fields intact