BWA alignment- Indexing of sorted BAM file

[gaurabSEQanswers]

Hi,

I have a problem with indexing the sorted BAM file in bwa alignment. I gave the command like this

samtools index ~/Desktop/Ruelliasorted.sorted.BAM and says that

EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file.

I need help to figure it out. Anybody out there???? Thanks in advance

[GenoMax]

See this old thread. How did you make your SAM/BAM file?

[gaurabSEQanswers]

bwa mem ~/Desktop/Tri.fasta ~/Desktop/R4A2R1.fastq ~/Desktop/R4A2R2.fastq >~/Desktop/RSAM.SAM for SAM file[

samtools view -b -S -o ~/Desktop/RBAM.BAM ~/Desktop/RSAM.SAM for BAM file

sorting- samtools sort ~/Desktop/RBAM.BAM >~/Desktop/RBAM.sorted.BAM

and i dont know how to figure out the problem in indexing.

[GenoMax]

What version of samtools are you using? Use the latest (v.1.5) if possible. Sorting with that version is done as follows

samtools sort -o sorted.bam original.bam
#then index
samtools index sorted.bam