**40**wrote:

Hi, I have a bam file. Then, to extract specific regions of that file, I used the command

```
cat chrs.txt | xargs -n 1 samtools view -@ 10 -b -h bd.bam > bd2.bam
```

where `chrs.txt`

is the file containing the regions to be exacted, like

chr1

chr1_random

chr2

Then, after got the bd2.bam file containing the extracted regions. I wanted to sort and index it. But an error happened here

samtools sort: truncated file. Aborting

I didn't know the reason, but on the other hand, if I generated another regional bam file using command like

```
samtools view -@ 10 -b -h bd.bam 'chrY'> bd3.bam
```

This time the bd3.bam file could be sorted normally. I don't know why encounter such an error. Does anyone know the reason?

Thank you.

The header information is

```
@HD VN:1.4 SO:coordinate
@SQ SN:BK000964 LN:45957
@SQ SN:chr10 LN:129993255
@SQ SN:chr11 LN:121843856
@SQ SN:chr12 LN:121257530
@SQ SN:chr13 LN:120284312
@SQ SN:chr13_random LN:400311
@SQ SN:chr14 LN:125194864
@SQ SN:chr15 LN:103494974
@SQ SN:chr16 LN:98319150
@SQ SN:chr16_random LN:3994
@SQ SN:chr17 LN:95272651
@SQ SN:chr17_random LN:628739
@SQ SN:chr18 LN:90772031
@SQ SN:chr19 LN:61342430
@SQ SN:chr1 LN:197195432
@SQ SN:chr1_random LN:1231697
@SQ SN:chr2 LN:181748087
@SQ SN:chr3 LN:159599783
@SQ SN:chr3_random LN:41899
@SQ SN:chr4 LN:155630120
@SQ SN:chr4_random LN:160594
@SQ SN:chr5 LN:152537259
@SQ SN:chr5_random LN:357350
@SQ SN:chr6 LN:149517037
@SQ SN:chr7 LN:152524553
@SQ SN:chr7_random LN:362490
@SQ SN:chr8 LN:131738871
@SQ SN:chr8_random LN:849593
@SQ SN:chr9 LN:124076172
@SQ SN:chr9_random LN:449403
@SQ SN:chrM LN:16299
@SQ SN:chrUn_random LN:5900358
@SQ SN:chrX LN:166650296
@SQ SN:chrX_random LN:1785075
@SQ SN:chrY LN:15902555
@SQ SN:chrY_random LN:58682461
@PG ID:STAR PN:STAR VN:STAR_2.5.3a CL:STAR ...
@CO user command line: STAR ...
```

**8.1k**• written 2.0 years ago by yuabrahamliu •

**40**