jfarek / xatlas Goto Github PK

Hi

Thanks for the great tools.
Is there any recommendation (or capability in xatlas) to merge single sample vcf produced by xatlas to the multi sample vcf.
I have tried several possibility:

• Run the xatlas in vcf mode and then combined using a simple bcftools merge . But there is a no way to differentiate between no call ./. to the homozygous reference 0/0 and i found that bcftools infers all non-variants site to be missing
• Run the xatlas in gvcf mode and then combined using gvcftools merge_variants. However, the gvcftools does not recommended to do this
  I am usually do imputation after variant calling. Thus the differentiation between non-ref and missing is important.

Thanks in advance for the help.

Hi Jesse,

What about xatlas' memory usage?
I just run it with my WES data (average coverage depth of 30x) and xatlas consumed 180G memory (RES) and 318G (VIRT) before I kill it. The log shows it's Processing records for region 3:197954977-197955050.

The command I used:

xatlas -r $hg19 -i wes.bam -s wes -p wes -t 8 -c $wes_bed -m 50 -n 25 -M 300 -z

Best,
Richard

It would ease installation to have an example of downloading a compatible HTSlib and pointing the configure at it.

I have tried multiple variants of the below and do not know what to expect or where it wants htslib/hts.h to be present. Linking ln -s does not work

cheers

./configure --enable-multithreading --with-htslib-lib=htslib-1.4.1
rcug@hpc03:/mnt/ngsnfs/tools/xatlas$ ./configure --enable-multithreading --with-htslib-lib=htslib-1.4.1
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking htslib/hts.h usability... no
checking htslib/hts.h presence... no
checking for htslib/hts.h... no
configure: error: Failed to find HTSLib headers

I have the latest version of htslib installed from http://www.htslib.org/download/ (v1.9), but when I try to run xatlas, I get the following error:

/xatlas: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory

Any suggestions?

Hello,

I would like to try your tool, but I ran into installation problems. I have htslib/1.4.1, but here is the error I got:

Xatlas.cpp:864:23: error: request for member ‘second’ in ‘coord’, which is of non-class type ‘const int’
if (coord.second > max_len) {
^
Xatlas.cpp:865:33: error: request for member ‘second’ in ‘coord’, which is of non-class type ‘const int’
max_len = coord.second;
^
Xatlas.cpp:877:10: error: ‘args_s’ has no member named ‘min_indel_mapq’
args.min_indel_mapq = min_indel_mapq;
^
Xatlas.cpp:878:10: error: ‘args_s’ has no member named ‘min_snp_mapq’
args.min_snp_mapq = min_snp_mapq;
^
Xatlas.cpp:889:30: error: ‘opts_s’ has no member named ‘snp_near_end_bases’
EventScanner events(opts.snp_near_end_bases, snp_max_sub, snp_max_indel);
^
make: *** [Xatlas.o] Error 1